A number of organometallic transformations related to proposed elementary steps in the reductive polymerization of carbon monoxide are discussed. The use of isonitrile as model ligands for carbon monoxide, with which they are isoelectronic, is proposed. Investigations show that alkyl migration to isonitrile is preferred over migration to carbon monoxide. Iminoformyl products due to hydride migration to isonitrile are not, however, observed. Syntheses of a range of cationic complexes of the type [ (η⁵-C₅H₅)M(L)₂(CNR)]⁺, [(η⁵-C₉H₇)Ru(L)₂(CNR)]⁺ and [(η⁵-C₉H₇)M(L)₂(CO)]⁺ (M = Fe, Ru; L = CO, phosphine) are described. In two cases, addition of hydride to the isonitrile cations is followed by protonation on work-up to give aminocarbene complexes. These are inert to further reduction under the conditions employed. The majority of isonitrile cations lose the isonitrile ligand to give good yields of metal hydride complexes. A mechanism involving ring-slippage of the hydrocarbon ligand is implicated. Hydride addition to η⁵-C₉H₇ complexes results, in the majority of cases, in loss of the hydrocarbon ligand from the complex and recovery of indane. Evidence for the intermediacy of metal formyl complexes in a number of hydride donation reactions is presented. These formyl complexes are formed from carbonyl hydride complexes either under moderate CO pressure or in THF solution. Hydride complexes lacking a carbonyl ligand are found to be inert. Finally, two reactions, one involving an alkyl migration reaction catalyzed by silver(I) salts, and the other involving the reduction of a metal acyl ligand to metal alkyl, are combined to demonstrate a model for carbon chain growth at a metal centre. The synthesis of an iron pentanoyl complex, followed by a decomplexation reaction, gives pentanoic acid in which all the catbon atoms are potentially directly derived from carbon monoxide. This is the first synthesis of a single homologous acid from carbon monoxide.

This thesis concerns the development of novel catalytic approaches for the construction of stereocentres bearing a nitrogen atom. In 2011, the Dixon group reported a Ag(I)/cinchona-derived amino phosphine catalytic system for the activation of isocyanoacetates in asymmetric aldol and Mannich reactions. During this thesis work it was sought to extend the scope of this catalytic system to Mannich additions of other isocyanide pronucleophiles, then the focus was broadened to include Reformatsky and α-alkylation reactions of ketimine substrates. Chapter 1 gives an overview of the state of the art with particular emphasis on catalytic enantioselective additions to ketimines and the use of activated isocyanides as pronucleophiles. Chapter 2 describes the application of the Ag-catalysed enantio- and diastereoselective aldol reaction of isocyanoacetates to the concise asymmetric synthesis of the antibiotic chloramphenicol, which possesses a chiral stereodefined α-amino β-hydroxy motif. Chapter 3 details our efforts to expand the scope of the Ag(I)/amino phosphine catalytic system to the activation of more challenging isocyanides lacking an electron-withdrawing group in the α-position by investigating aldol and Mannich reactions of benzyl isocyanide. Chapter 4 describes how the scope of the Ag(I)/amino phosphine catalytic system was successfully extended to another pronucleophile, the versatile p-toluenesulfonylmethyl isocyanide (TosMIC). The first catalytic enantio- and diastereoselective addition of TosMIC to N-diphenylphosphinoyl (N-DPP) ketimines was developed, affording 2-imidazolines possessing two contiguous stereocentres with high yields and excellent levels of stereocontrol. Chapter 5 describes the development of a Ni(II)-catalysed Reformatsky reaction of N-DPP ketimines with ethyl bromoacetate and diethylzinc, providing racemic amines bearing a quaternary stereocentre in the α-position in good yields. Chapter 6 reports the serendipitous discovery of the α-alkylation of N-DPP ketimines with ethyl bromoacetate using visible light photoredox catalysis. The transformation, catalysed by ruthenium(II) and nickel(II) complexes under mild conditions, was optimised, its scope assessed and the mechanism investigated.

The development of Plasmodium falciparum malarial resistance to the current armoury of anti-malarial drugs requires the development of new treatments to help combat this disease. The marine environment is a well established source of potential pharmaceuticals. Of interest to us are isonitrile, isocyanate and isothiocyanate compounds isolated from marine sponges and molluscs which have exhibited nano-molar anti-plasmodial activities. Through quantitative structure-activity relation studies (QSAR), a literature precedent exists for a pseudoreceptor model from which a pharmacophore for the design of novel anti-malarial agents was proposed. The current theory suggests that these marine compounds exert their inhibitory action through interfering with the heme detoxification pathway in P. falciparum. We propose that the computational methods used to draw detailed conclusions about the mode of action of these marine compounds were inadequate. This thesis addresses this problem using contemporary computational methodologies and seeks to propose a more robust method for the rational design of new anti-malarial drug compounds that inhibit heme polymerization to hemozoin. In order to investigate the interactions of the marine compounds with their heme targets, a series of modern computational procedures were formulated, validated and then applied to theoretical systems. The validations of these algorithms, before their application to the marine compound-heme systems, were achieved through two case studies. The first was used to investigate the applicability of the statistical docking algorithm AutoDock to be used for the exploration of conformational space around the heme target. A theoretical P. falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (PfDXR) enzyme model, constructed by the Biochemistry Department at Rhodes University, provided the ideal model to validate the AutoDock program. The protein model was accordingly subjected to rigorous docking simulations with over 30 different ligand molecules using the AutoDock algorithm which allowed for the docking algorithm’s limitations to be ascertained and improved upon. This investigation facilitated the successful validation of the protein model, which can now be used for the rational design of new PfDXR-inhibiting anti-plasmodial compounds, as well as enabling us to propose an improvement of the docking algorithm for application to the heme systems. The second case study was used to investigate the applicability of an ab initio molecular dynamics algorithm for simulation of bond breaking/forming events between the marine compounds and their heme target. This validation involved the exploration of intermolecular interactions in a naturally occurring nonoligomeric zipper using the Car-Parrinello Molecular Dynamics (CPMD) method. This study allowed us to propose a model for the intermolecular forces responsible for zipper self-assembly and showcased the CPMD method’s abilities to simulate and predict bond forming/breaking events. Data from the computational analyses suggested that the interactions between marine isonitriles, isocyanates and isothiocyanates occur through bond-less electrostatic attractions rather than through formal intermolecular bonds as had been previously suggested. Accordingly, a simple bicyclic tertiary isonitrile (5.14) was synthesized using Kitano et al’s relatively underutilized isonitrile synthetic method for the conversion of tertiary alcohols to their corresponding isonitriles. This compound’s potential for heme detoxification inhibition was then explored in vitro via the pyridine-hemochrome assay. The assay data suggested that the synthesized isonitrile was capable of inhibiting heme polymerization in a similar fashion to the known inhibitor chloroquine. Attempts to synthesize tricyclic analogues of 5.14 were unsuccessful and highlighted the limitation of Kitano et al’s isonitrile synthetic methodology.

Student Number : 0009404H - PhD thesis - School of Chemistry - Faculty of Science / Six-coordinate ruthenium complexes of the type ttt-RuX2(RNC)2(PPh3)2 (X = Cl ; R = tBu, 2,6-xylyl, benzyl, 2-OMe-4-Clphenyl and iPr; X = Br; R = = tBu, 2,6-xylyl, benzyl, iPr ) were synthesized and fully characterised by IR, NMR spectroscopy and elemental analysis. These complexes were all found to undergo solid-state isomerisation from the ttt-isomer to the cct-isomer. It was found that solid state isomerisation occurred before melting i.e. in the solid state for all the ttt-RuX2(RNC)2(PPh3)2 complexes investigated . The thermal solid state isomerisation process was monitored by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), thermomicroscopy and X-ray powder diffraction techniques. The results revealed that the isomerisation process occurred exothermally with darkening of the crystal. A mechanism which involved rotation of small ligands was proposed to explain the solid-state isomerisation process. Kinetic studies of the solid-state isomerisation of some of the ttt-RuCl2(RNC)2(PPh3)2 complexes were carried out and monitored by NMR spectroscopy and compared with kinetic studies performed by XRD methods. The results are similar and also suggest that the isomerisation reaction follows first order kinetics. The crystal and molecular structure of ttt-RuCl2(2,6-xylylNC)2(PPh3)2 was determined by X-ray single crystal diffraction techniques and its structure was compared with related ttt- RuX2(RNC)2(PPh3)2 complexes. Inter-molecular and intra-molecular interactions in these molecules in the solid state were analysed and used to rationalise the solid-state isomerisation results. The results obtained for the ruthenium complexes suggested that other six-coordinate complexes could undergo solid state isomerisation reactions and this study was extended to molybdenum complexes of the type cis-Mo(CO)4L2. These complexes undergo cis to trans isomerisation in solution. The solid state reactivity of these complexes was investigated for the first time. The complexes with L = PPh2Me and PPh2Et isomerised in the melt whist complexes with L = PPh3 amd P(m-tolyl)3 were indeed found to undergo solid state isomerisation reactions. Structural studies and thermomicroscopic investigations were done on cis- Mo(CO)4(PPh3)2 and Mo(CO)4{P(m-tolyl)3)2 and the results were used to rationalize the solid state reactivity of these complexes.

Organometallic chemistry is a powerful tool for the coupling of simple unsaturated molecules to form complex organic structures. Isonitriles (RNCs) are an attractive alternative to isoelectronic CO as C₁ sources in the pursuit of C,C coupling reactions. The electronic properties of the substituent on nitrogen in RNCs can bring about insertion chemistry that is different from the insertion reactions of CO. The insertion chemistry of RNCs with Group 4 (Ti, Zr, and Hf) butadiene complexes will be described. Cp*(Cl)Ti(2,3-dimethylbutadiene) (2.1) reacts with two equivalents of RNC to give η¹,η²-diimine complexes 2.2 (R = ^tBu) and 2.3 (R = 1-adamantyl). Cp*(Cl)Ti (N,N-di-^tBu-η¹,η²-diimine) (2.2), in the presence of pyridine, fragments to Cp*(Cl)Ti(NtBu)(NC₅H₅) (2.10) and an α-methylene cyclopent-3-enimine 2.11. The hafnium analog of 2.1, Cp*(Cl)Hf(2,3-dimethylbutadiene) (2.14), has been reported to give a cyclic amidine complex when treated with two equivalents of 2,6-dimethylphenyl isonitrile. By X-ray crystallography, however, this work finds that 2.14 and 2,6-dimethylphenyl isonitrile give instead a 2,5-diazahafnacyclopentane that features a σ-interaction between the C¬–C bond of a cyclopropane ring and the Hf. Cp*₂Zr(2,3-dimethylbutadiene) (3.1) reacts with tert-alkyl isonitriles to give η²-iminoacyl complexes Cp*₂⏞(⏟(Zr[CH₂ C(CH₃)C(CH₃)CH₂C)(NR)] 3.2 (R = tBu) and 3.3 (R = 1-adamantyl). Treatment of 3.2 with excess isopropyl isonitrile gives the η¹,η²-bis(iminoacyl) complex Cp*₂⏞(⏟(Zr[C(N^i Pr)CH₂ C(CH₃)C(CH₃)CH₂C)(N)iPr)] (3.4) and free tert-butyl isonitrile. The reaction of 3.1 with 2 equivalents of isopropyl isonitrile also affords 3.4, through the intermediate Cp*₂⏞(⏟(Zr[CH₂ C(CH₃)C(CH₃)CH₂C)(N^iPr)] (3.5). Carbonylation of 3.2 affords the Zr formimidoyl cyclopentadienolate 3.6. Treatment of a Zr hydride cyclopentadienolate (3.7), obtained from the carbonylation of 3.1, with tert-butyl isonitrile also affords 3.6. Isotopic labeling shows that the insertion of tert-butyl isonitrile into 3.1 and 3.7 is reversible.

This thesis is divided into two parts, assessing marine and synthetic compounds active firstly against Plasmodium falciparum (Chapter 3 and 4) and secondly active against methicillin resistant Staphylococcus aureus (MRSA, Chapter 5). In Chapter 3 the synthesis of nine new tricyclic podocarpanes (3.203-3.207 and 3.209-3.212) from the diterpene (+)-manool is described. Initial SAR study of synthetic podocarpanes concluded that the most active compound was a C-13 phenyl substituted podocarpane (3.204, IC₅₀ 6.6 μM). By preparing analogues with varying halogenated substituents on the phenyl ring (3.209-3.212) the antiplasmodial activity was improved (IC₅₀ 1.4 μM), while simultaneously decreasing the haemolysis previously reported for this class of compounds. Inspired by the antiplasmodial activity of Wright and Wattanapiromsakul’s tricycle marine isonitriles (2.16-2.21 and 2.24-2.27) an unsuccessfully attempt was made to convert tertiary alcohol moieties to isonitrile functionalities in compounds 3.188, 3.204-3.207 and 3.209-3.212. Over a decade ago Wright et al. proposed a putative antiplasmodial mechanism of action for marine isonitriles (2.4, 2.9, 2.15, 2.19 and 2.35) and isothiocyanate (2.34) which involved interference in haem detoxification by P. falciparum thus inhibiting the growth of the parasite. In Chapter 4 we describe how we successfully managed to scale down Egan’s β-haematin inhibition assay for the analyses of small quantities of marine natural products as potential β-haematin inhibitors. Our modified assay revealed that the most active antiplasmodial marine isonitrile 2.9 (IC₅₀ 13 nM) showed total β-haematin inhibition while 2.15 (IC₅₀ 81 nM) and 2.19 (IC₅₀ 31 nM) showed partial inhibition at three equivalents relative to haem. Using contempary molecular modelling techniques the charge on the isonitrile functionality was more accurately describe and the modified charge data sets was used to explore docking of marine isonitriles to haem using AutoDock. In Chapter 5 we describe how a lead South African marine bisindole MRSA pyruvate kinase inhibitor (5.8) was discovered in collaboration with colleagues at the University of British Columbia (UBC) and how this discovery inspired us to design a synthetic route to the dibrominated bisindole, isobromotopsentin (5.20) in an attempt to increase the bioactivity displayed by 5.8. We devised a fast and high yielding synthetic route using microwave assited organic synthesis. We first tested this synthesis using simple aryl glyoxals (5.27-5.32) as precursors to synthesize biphenylimidazoles (5.21-5.26), which later allowed us to synthesize the ascidian natural product 5.111. This method was sucessfully extended to the synthesis of deoxytopsentin (5.33) from an N-Boc protected indole methyl ketone (5.89). We subsequently were able to effectively remove the carbamate protection via thermal decomposition by heating the protected bisindole imidazole (5.90) in a microwave reactor for 5 min under argon. The synthesis of 5.20 resulted in an inseparable mixture of monoprotected and totally deprotected topsentin products, and due to time constraints we were not able to optimise this synthesis. Nonetheless our synthesis of the marine natural product 5.33 which was faster and higher yielding than previously reported routes could be extended to the synthesis of other topsentin bisindoles (5.138-5.140). Work towards this goal continues in our laboratory.

Les réactions multicomposant à base d'isonitrile (I-MCR) combinées à des transformations de post-condensation constituent des outils de synthèse extrêmement puissants pour la préparation de structures moléculaires complexes et diverses avec de nouvelles propriétés pharmacologiques.Dans un premier temps, nous nous sommes intéressés à l'extension du couplage de Ugi-Smiles aux dérivés de purines, en utilisant la 6-mercaptopurine comme partenaire de couplage. Cette méthodologie permet un accès direct et rapide aux dérivés d'adénine avec des rendements modérés à bons à partir de précurseurs simples et facilement accessibles.Par la suite, nous avons démontré que les produits d'addition Ugi dérivés d'aldéhydes aromatiques peuvent être convertis en 2-pyrrolines par addition d'accepteurs de Michael, sous irradiation par micro-ondes. La réaction peut se dérouler via la formation inhabituelle d’ylures azométhines suivie d'une cycloaddition [3 + 2] avec des accepteurs de Michael.Enfin, nous avons montré que les adduits Passerini issus de cinnamaldéhyde peuvent être efficacement convertis en α-cétoamides lorsqu'ils sont traités en milieu basique et dans des conditions de chauffage sous irradiations micro-ondes. / The isocyanide based multicomponent reactions (I-MCRs) with subsequent post-condensation transformations constitute extremely powerful synthetic tools for the preparation of structurally diverse complex molecules with novel properties.In this context, we first investigated the extension of Ugi-Smiles coupling to purines, by using 6-mercaptopurine as coupling partner. This methodology allows direct access to adenine derivatives in moderate to good yields starting from readily available precursors.Then, we demonstrated that Ugi adducts derived from aromatic aldehydes may be converted to pyrrolines via addition of Michael acceptors under microwave irradiation. The reaction may proceed via unusual formation of azomethine ylides followed by a [3+2] cycloaddition using Michael acceptors.Finally, we described that the Passerini adducts of cinnamaldehyde and analogues may be efficiently converted into α-ketoamides when heated with a base under microwave conditions.

Les réactions de type Ugi sont connues depuis une cinquantaine d’années. Ces réactions multicomposants mettent en jeu un aldéhyde, une amine, un isonitrile ainsi qu’un dérivé acide (acide carboxylique ou phénol activé). Dans ces travaux, la structure électronique des isonitriles, composé au coeur de ces réactions a été étudiée. La forme carbénique RN=C s’est révélée majoritaire contrairement à toute attente. La linéarité de la molécule a pu être interprétée grâce aux contributions des formes minoritaires. La seconde partie s’est focalisée sur l’étude théorique et expérimentale des couplages de type Ugi. Contrairement à la réaction de Ugi-Smiles, le réarrangement final de la réaction de Ugi, un réarrangement de Mumm, s’est révélé non cinétiquement déterminant. L’importance du rôle de l’environnement a été étudiée par le biais d’une microsolvatation. La compréhension accrue de la réaction de Ugi-Smiles a fait émerger deux nouveaux partenaires acides : les trichlorophenols et les nitrosophenols. Les premiers ont permis d’isoler pour la première fois desaryl-imidates de phénol. Les seconds ont été utilisés pour développer une nouvelle voie de synthèse debenzimidazoles à partir des adduits de Ugi-Smiles correspondants. Enfin, les adduits de type Ugi ont été mis à profit pour développer une nouvelle réaction palladocatalysée d’ouverture d’aminocyclopropanes. Cette ouverture conduit à l’accès rapide de produits hétérocycliques dont des tétracycles complexes suite à une réaction tandem impliquant un couplagede Heck. / Ugi type reactions are well known for decades. These multicomponent reactions involve an aldehyde,an amine, an isocyanide and an acid compound (carboxylic acid or activated phenol). Herein, electronicstructure of isocyanides, as key compounds of these reactions, was studied. Surprisingly, thecarbenic form RN=C was found to be the major one. Contribution of minor mesomeric structureexplains the linearity of the molecule. Then, Ugi and Ugi-Smiles couplings were studied theoreticallyand experimentally. Contrary to the Ugi-Smiles reaction, the final rearrangement of the Ugi coupling,a Mumm one, was not found to be a rate determining step. Importance of microsolvation was investigated.The comprehension of the mechanism of Ugi-Smiles reaction prompted us to investigatetheoretically new acidic partners. Trichlorophenols permitted to isolate the aryl-imidate for the firsttime with a phenol. Nitrosophenols were also considered. Confirmed experimentally, these new adductswere used to propose a new synthesis of benzimidazole. Finally, Ugi type adducts have been used todevelop a new palladium-catalyzed ring-opening of aminocyclopropanes. Rapid access to heterocycliccompounds, such as complex tetracycle with a tandem Heck coupling, can be obtained by this strategy.

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