The synthesis of pure tris(6-hydroxymethyl-2-pyridylmethyl)amine (H₃L₁₁) is reported for the first time. New complexes of H₃L₁₁ with copper(II), manganese(II) and iron(III) have been characterised by X-ray crystallography. Linear [Fe₃(L₁₁)₂](ClO₄)₃ reveals the tightest Fe-O-Fe angle (87.6°) and shortest Fe...Fe distance (2.834 Å) presently found for a weakly antiferromagnetically-coupled high spin alkoxide-bridged polyiron(III) system. H₃L₁₁ provides a route to various hydrophobic peralkylated TPA ligand derivatives for creating a hydrophobic pocket for the assembly of iron catalysts for the novel 1-hydroxylation of n-alkanes. New 6-py substituted TPA ligands containing methyl (L₁₅) and n-octyl (L₁₆) ether linkages were synthesised via alkylation. Two further novel 6-py substituted ligands were synthesized incorporating n-hexyl substituents on one (L₂₁) and two (L₂₂) of the py moieties. Here a urea spacer group was used to promote hydrogen–bond assisted heterolytic O-O cleavage (generation of the potent FeV=O oxidant) within the hydroxoperoxoiron(III) precursor. High spin [FeII(L)(CH₃CN)[subscript(x)]](CF₃SO₃)₂ complexes (x = 0–2, L = L₁₅,₁₆,₂₁,₂₂) were characterised in solution by ¹H NMR. The structure of [Fe(L₂₂)](CF₃SO₃)₂ reveals a distorted iron(II) centre bound to four N atoms and two urea carbonyls. Iron(II) complexes of H₃L₁₁, L₁₅,₁₆,₂₁,₂₂ and tris(6-Br)-TPA (L₂₄), were investigated for catalysis of the oxygenation of cyclohexane by H₂O₂. Reaction of the iron(II) complexes with H₂O₂ and [superscript(t)]BuOOH was followed by time-resolved EPR and UV-VIS spectrophotometry. A correlation between the observed catalytic activity and the nature of the FeIII(L)-OOR intermediates generated is apparent. A convenient ‘one-pot’ synthesis of benzene-1,3,5-triamido-tris(l-histidine methyl ester) is reported along with attempts at preparing N,N’-bis(pyridylmethyl)-1,3- diaminopropane-2-carboxylic acid (L₂₅), a new water soluble pyridine-amine ligand. The final demetallation step resulted in ligand hydrolysis to the novel amino acid; 1,3-diaminopropane- 2-carboxylic acid which was characterised as its HCl salt by X-ray crystallography.

Les monooxygénases à cuivre sont des systèmes enzymatiques capables de transférer un atome d'oxygène à leur substrat de manière hautement régio et stéréo-spécifique. Les complexes modèles de monooxygénases à cuivre ont fourni de précieuses informations sur la structure et la réactivité des espèces «cuivre-dioxygène» impliquées dans une telle réactivité. Cependant, la découverte récente de deux nouveaux systèmes enzymatiques (LPMO et pMMO) capables d'effectuer l'activation des liaisons C-H très énergétiques a réouvert le débat sur les espèces cuivre--oxygène capables d'une telle réactivité. Dans ce travail, nous avons choisi de préparer des complexes bio-inspirés de Cu(I) et Cu(II) avec un ligand contenant un substrat interne. Ces complexes ont été exposés à différents oxydants ou donneurs d'atome d'oxygène et nous avons étudié la régio- et stéréo-sélectivité de la réaction d'oxydation du substrat interne. De plus, nous avons évalue la capacité de ces systèmes à utiliser l'eau comme donneur d'atome d'oxygène. Pour cela, nous avons l'oxydation ou l'activation de l'eau par voie électrochimique afin de générer des intermédiaires cuivre-oxygène conduisant éventuellement à la production de dioxygène ou à l'oxydation sélective du ligand. Enfin, nous nous sommes intéressés aux propriétés d'espèces hétérobimétalliques à haute valence. Par conséquent, deux nouveaux complexes hétérobimétalliques à haute valence contenant du nickel et du cuivre ont été synthétisés. Nous avons étudié leurs propriétés électroniques et leur réactivité envers des substrats externes et internes (ligands) a été évaluée et comparée à la réactivité de leurs homologues homobimétalliques. / Copper-containing monooxygenases are enzymatic systems capable of transferring an oxygen atom to their subtrates in highly regio or stereo-specific modes. Model complexes for copper-containing monooxygenases have provided valuable information on the structure and reactivity of several copper-dioxygen adducts. However, the recent discovery of two new enzymatic systems (LPMO and pMMO) able to perform activation of very strong C-H bonds has re-opened the debate on the catalytically relevant copper-dioxygen species. The use of model systems that mimic an enzyme is a simple approach to obtain a better knowledge of how nature works. For this study, Cu(I) and Cu(II) complexes containing ligand-substrate were prepared. After reaction with different oxidants or O-atom donors, we investigated the regio- and stereo-selectivity of the oxidation of the internal substrate. Based on the relatively well-known chemistry of Cu(I) with dioxygen, we, were also interested in investigating the water as an O-atom donor in C-H bond activation reactions. We have therefore investigated electrochemical water oxidation or activation to generate dioxygen and selective oxygen-insertion into the substrate-bound moiety. Finally, we explored the properties of mixed-metal dioxygen species as compared to their homometalic counter-parts. Indeed heterobimetallic active sites are found in various metalloenzymes such as cytochrome c oxidase. Therefore, two new high-valent Cu-Ni heterobimetallic complexes were synthesized. We investigated their electronic properties using various spectroscopic methods and their reactivity was evaluated towards external and internal substrates (indane).

L’oxydation catalytique des liaisons C-H, en condition aérobie est l’une des réactions « phare » de la chimie, aussi bien d’un point de vue fondamental qu’industriel. Le principal défi consiste en l’utilisation de l’oxygène moléculaire comme oxydant « vert » pour l’activation de ces liaisons C-H. De nombreuses métalloprotéines, telles que les mono-oxygénases (Fe, Cu), sont capables de réaliser ces réactions dans des conditions douces. Une stratégie actuelle consiste à développer des systèmes synthétiques capables de reproduire de manière efficace les propriétés catalytiques de ces enzymes. L’objectif principal de nos travaux a été de synthétiser et de caractériser des modèles de mono-oxygénases solubles (sMMO) et membranaires (pMMO). Deux approches ont été développées. La première a consisté à élaborer des ligands ditopiques dissymétriques, dont les deux sites de coordination tris-(2-pyridymethyl)amine “TPA” et pyridinedicarboxamide “PydCA”, sont enclavés dans un seul macrocycle afin de favoriser une distance intermétallique optimale. La seconde stratégie est basée sur la synthèse de ligands ditopiques où les motifs coordinants, tetraazacyclotetradecane “cyclam” et dipicolylamine “DPA”, sont séparés par un espaceur de type phényle. Ces deux approches ont conduit à l’obtention et à la caractérisation, à l’état solide (structure aux rayons X) et en solution (spectroscopie, électrochimie), de nombreux complexes mono et dinucléaires du fer, du cuivre et du cobalt. L’étude de la réactivité de certains complexes mononucléaires vis-à-vis des oxydants tels que O2 et H2O2, en l’absence de substrats organiques, a permis d’identifier des espèces métal-oxygène. L’oxydation catalytique de substrats organiques a également été réalisée. / Catalytic oxydation of C-H bonds using molecular oxygen as ‘green’ oxidant remains a great challenge from both fundamental and industrial point of views. Many metalloproteins, such as copper end iron-based mono-oxygenases are able to perform these reactions under mild conditions. A current strategy is to develop synthetic complexes which can reproduce the efficiency of such enzymes. The main objective of our work has been to synthesize and characterize new models of soluble (sMMO) and particulate (pMMO) mono-oxygenases. Two approaches have been developed. The first strategy was to synthesize unsymmetrical dinucleating ligands bearing two coordination sites, tris-(2-pyridylmethyl)amine “TPA” and pyridinedicarboxamide “PydCA”, which are embedded in a single macrocycle to favor intermetallic interaction. The second strategy is based on the synthesis of dinucleating ligands where coordinating patterns, tetraazacyclotetradecane “cyclam” and dipicolylamine “DPA”, are separated by a phenyl type spacer. These two approaches have led to the formation and characterization in the solid state (X-ray structure) and in solution (spectroscopy, electrochemistry) of many mononuclear and dinuclear iron, copper and cobalt complexes. The study of the reactivity of some mononuclear complexes towards oxidants such as O2 and H2O2, in absence of organic substrates, has led to the identification of metal-oxygen species. Catalytic oxidation of organic substrates was also conducted.

This thesis describes the synthesis, characterisation and application of artificial metalloenzymes as catalysts. The focus was on two mutants of SCP-2L (SCP-2L A100C and SCP-2L V83C) both of which possess a hydrophobic tunnel in which apolar substrates can accumulate. The crystal structure of SCP-2L A100C was determined and discussed with a special emphasis on its hydrophobic tunnel. The SCP-2L mutants were covalently modified at their unique cysteine with two different N-ligands (phenanthroline or dipicolylamine based) or three different phosphine ligands (all based on triphenylphosphine) in order to increase their binding capabilities towards metals. The metal binding capabilities of these artificial proteins towards different transition metals was determined. Phenanthroline modified SCP-2L was found to be a promising scaffold for Pd(II)-, Cu(II)-, Ni(II)- and Co(II)-enzymes while dipicolylamine-modified SCP-2L was found to be a promising scaffold for Pd(II)-enzymes. The rhodium binding capacity of two additional phosphine modified protein scaffolds was also investigated. Promising scaffolds for Rh(I)- and Ir(I)-enzymes were identified. Rh-enzymes of the phosphine modified proteins were tested in the aqueous-organic biphasic hydroformylation of linear long chain 1-alkenes and compared to the Rh/TPPTS reference system. Some Rh-enzymes were found to be several orders of magnitude more active than the model system while yielding comparable selectivities. The reason for this remarkable reactivity increase could not be fully elucidated but several potential modes of action could be excluded. Cu-, Co-, and Ni-enzymes of N-ligand modified SCP-2L A100C were tested in the asymmetric Diels-Alder reaction between cyclopentadiene and trans-azachalcone. A promising 29% ee for the exo-product was found for the phenanthroline modified protein in the presence of nickel. Further improvement of these catalyst systems by chemical means (e.g. optimisation of ligand structure) and bio-molecular tools (e.g. optimisation of protein environment) can lead to even more active and (enantio)selective catalysts in the future.

Metallohydrolases with dinuclear-zinc active sites perform many important biological hydrolytic reactions on a variety of substrates. In this regard, metallo-β-lactamases (mβ1, class B) represent a unique subset of zine hydrolases that hydrolyze the β-lactam ring in several antibiotics. The antibiotic resistance that results from this hydrolysis is becoming an increased threat for the clinical community. These metalloenzymes can hydrolyze a wide range of β-lactam substrates, such as cephamycins and imipenem that are generally resistant t the serine-containing β-lactamases. Therefore, the clinical application of the entire range of antibiotics is severely compromised in bacteria that produce mβls. Due to the lack of information on the mechanism of mβls, to-date, no clinically known inhibitors is there for mβls. In this present study, we synthesized several mono and dizinc complexes as models for the mβls and investigated the differences in their hydrolytic properties. This study supports the assumption that the second zinc in the dinuclear enzymes does not directly involve in the catalysis, but may orient the substrates for hydrolysis and the basic amino acid residues such as Asp and His may activate the zinc-bound water molecules, fulfilling the role of the second zinc in the mononuclear enzymes. The effect of various side chains on the hydrolysis of some commonly used cephalosporin antibiotics by mβl from B.cereus is described. It is shown that the cephalosporins having heterocyclic thiol side chains are more resistance to mβl-mediated hydrolysis than the antibiotics that do not have such side chains. This is partly due to the inhibition of enzyme activity by the thiol moieties eliminated during the hydrolysis. It is also observed that the heterocyclic side chains in pure form inhibit the lactamase activity of mβl as well as its synthetic mimics. The mode of binding of these heterocyclic side chains to the zinc has been analyzed from the crystal structure of the tetranuclear zinc complexes. The theoretical studies suggest that the eliminated heterocyclic thiols undergo a rapid tautomerism to produce the corresponding thiones. These thiones are found to irreversibly inhibit the LPO-catalyzed iodination reaction. The reaction of various thiones with I2 leads to the formation of thione-iodine complexes similar to that of the most commonly used antithyroid drug methimazole(MMI). These observations suggest that some of the latest generation of antibiotics may show negative effects on thyroid gland upon hydrolysis. Synthetic organophosphorus compounds have been used extensively as pesticides and petroleum additives. These compounds are very toxic to mammals and their widespread use in agriculture leads to serious environmental problems. Therfore, degradation of organophosphorus trimesters and remediation of associated contaminated sites are of worldwide concern. In this regards, the bacterial phsophotriesterase (PTE) enzyme plays an important role in degrading a wide range of organophosphorus esters and the active side of PTE has been shown to be very similar to that of mβl. This identification prompted us to check the hydrolysis of phosphotriesters by the mβl and its mimics. It has been observed that the dinuclear zine(II) complexes that do not allow a strong binding of phosphodiestes would be a better PTE mimics.

No description available.

Les protéines à radical S-adénosyl-L-méthionine (SAM) utilisent un centre [Fe4S4] réduit pour initier le clivage réductive homolytique de la SAM et la formation d'une espèce hautement réactive - le radical 5'-déoxyadénosyl ou 5'-dA•. Dans la quasi-totalité de cas ce radical alkyl va arracher un atome d'hydrogène sur le substrat et déclencher ainsi sa conversion en produit. On trouve ces enzymes au niveau d'étapes clé de la synthèse de certaines vitamines, antibiotiques, précurseurs de l'ADN ou encore cofacteurs protéiques où elles sont souvent impliquées dans le clivage ou la formation des liaisons C-C, C-N, C-S ou encore C-P. Les travaux réalisés au cours de cette thèse ont été focalisés sur l'étude structurale et fonctionnelle de la protéine HydE ; une enzyme à radical SAM, qui intervient dans la biosynthèse du site actif organométallique de l'hydrogénase à [FeFe]. L'objectif principal était d'identifier le substrat de HydE et d'étudier les détails du fonctionnement d'une protéine à radical SAM. Nous avons réussi à identifier un groupe de molécules, dérivées de la cystéine, contentant un cycle thiazolidine avec un ou deux groupements carboxylates, qui ont une très bonne affinité pour le site actif de HydE. Certains de ces ligands se sont montrés d’être des substrats non physiologiques de l’enzyme. Grâce à ces substrats nous avons pu mettre en évidence un nouveau mécanisme d’attaque radicalaire dans les protéines à radical SAM. En effet, dans HydE nous avons observé une attaque directe du radical 5'-dA• sur l’atome soufre du thioéther appartenant au cycle thiazolidine. Cette réaction constitue un exemple pas comme les autres d’une insertion d’un atome de soufre (ou de sélénium) catalysée par une enzyme à radical SAM. Il s'agit également d'une première observation d'une réaction radicalaire dans les cristaux protéiques d'une enzyme à radical SAM et également un premier suivi en temps réel par la RMN du 13C et 1H de l'accumulation d'un des produits de la réaction catalysée par ces enzymes. Les résultats de calculs théoriques basés sur nos structures cristallographiques de haute résolution suggèrent que dans le cas de cette superfamille de protéines le radical 5'-dA• serait plutôt un état de transition et donc pas une espèce intermédiaire isolable. / Radical S-adenosyl-L-methionine (SAM) proteins use a reduced [Fe4S4] cluster to initiate homolytic reductive cleavage of SAM, which leads to the formation of highly reactive 5'-deoxyadenosyl radical species or 5'-dA•. In almost all cases this alkyl radical will abstract a hydrogen atom from the substrate and thus trigger its conversion into product. These enzymes are found in key steps of the synthesis of certain vitamins, antibiotics, DNA precursors or protein cofactors. They are often involved in the cleavage or formation of C-C, C-N, C-S or C-P bonds. The present thesis work has been focused on the structural and functional study of HydE protein; a radical SAM enzyme, involved in the biosynthesis of the organometallic active site of [FeFe]-hydrogenase. The main goal was to identify the substrate of HydE and to study details of how radical SAM proteins control the highly oxidizing 5'-dA• species. We managed to identify a group of molecules, derived from cysteine, containing a thiazolidine ring with one or two carboxylate groups, which have a very good affinity for the active site of HydE. We have demonstrated some of these ligands are non-physiological substrates of the enzyme. With these substrates we could highlight a new radical attack mechanism in radical SAM proteins. Indeed, in HydE we observed a direct attack on the 5'-dA • radical on the sulfur atom of the thioether belonging to the thiazolidine ring. This is an unprecedented reaction that contrasts with sulfur (or selenium) atom insertion reactions catalysed by some radical SAM enzymes. This is also the first observation of a radical reaction in the protein crystal of a radical SAM enzyme and also the first real-time monitoring by 1H- & 13C-NMR spectroscopy of the accumulation of products of the reaction catalysed by these enzymes. Theoretical calculations based on our high-resolution crystal structures suggest that in the case of this protein superfamily the 5'-dA• radical, which triggers the reaction in radical SAM enzymes, is a transition state and therefore not an isolable intermediate species.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-05-04T19:26:38Z No. of bitstreams: 1 lucasfagundesesteves.pdf: 10750065 bytes, checksum: 8871e6f0092a5a329a1cc8099f9a0382 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-05-17T13:33:34Z (GMT) No. of bitstreams: 1 lucasfagundesesteves.pdf: 10750065 bytes, checksum: 8871e6f0092a5a329a1cc8099f9a0382 (MD5) / Made available in DSpace on 2017-05-17T13:33:34Z (GMT). No. of bitstreams: 1 lucasfagundesesteves.pdf: 10750065 bytes, checksum: 8871e6f0092a5a329a1cc8099f9a0382 (MD5) Previous issue date: 2016-02-29 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Esta tese propõe uma investigação teórica do mecanismo de quebra hidrolítica de um modelo para diésteres de fosfato, o íon BDNPP [bis(2,4-dinitrofenil)fosfato], catalisada por um complexo dinuclear de cobre(II) (R1). Esse complexo metálico foi originalmente planejado para mimetizar a estrutura e as propriedades catalíticas do sítio ativo das catecóis oxidases (COs), revelando um caso interessante de promiscuidade catalítica em sistemas biomiméticos. As possibilidades de mecanismo foram cuidadosamente avaliadas através de cálculos de Teoria do Funcional da Densidade (DFT) em fase gás e em fase aquosa com cálculos no ponto dentro do modelo contínuo polarizável (PCM). Dois mecanismos principais foram encontrados. O Mecanismo 1 (Concertado) corresponde a uma reação do tipo SN2 que envolve o ataque da ponte µOH, situada entre os íons Cu(II), ao centro fosfórico da molécula de BDNPP, enquanto que o Mecanismo 2 (Associativo) ocorre através de sucessivas transferências de próton entre o átomo de oxigênio desta mesma ponte com o átomo de oxigênio terminal do grupo fosfato, passando pela formação de um intermediário pentacoordenado estável. O Mecanismo 1 envolve dois possíveis caminhos reacionais para a liberação do íon DNPP [(2,4-dinitrofenil)fosfato] gerado após a quebra hidrolítica. O primeiro caminho reacional (p1) envolve uma transferência de próton – que ocorre entre o átomo de oxigênio que compunha a ponte µ-OH e o átomo de oxigênio terminal do grupo fosfato – imediatamente após a quebra hidrolítica, seguido pela entrada de duas moléculas de água, sendo a etapa de transferência de próton determinante da velocidade. O segundo caminho reacional (p2) envolve a entrada de duas moléculas de água imediatamente após a quebra hidrolítica sem que haja a reação de transferência de próton, sendo a etapa de quebra hidrolítica a etapa determinante da velocidade. Dentre as propostas de mecanismo estudadas o caminho reacional p2 dentro do Mecanismo 1 corresponde ao mais provável, uma vez que possui a menor barreira de reação (ΔG‡ = 23,7 kcal mol-1, em solução aquosa). A constante de velocidade observada experimentalmente, Kobs, vale 1,7 × 10-5 s-1, indicando que o valor calculado teoricamente (K1 = 2.6 × 10-5 s-1) está em excelente acordo com o valor experimental. O efeito isotópico cinético (KIE) foi avaliado para o caminho reacional p2 dentro do Mecanismo 1 com o intuito de entender as alterações estruturais envolvidas na formação do TS1-i (Estado de transição para o Mecanismo 1), caracterizando perfeitamente o mecanismo descrito. O efeito explícito da inclusão de moléculas do solvente foi avaliado de maneira preliminar para apenas uma estrutura do ciclo catalítico para a quebra hidrolítica de ésteres de fosfato, através da utilização do método de Monte Carlo. Os resultados permitem uma análise detalhada da organização das moléculas de solvente ao redor do complexo, podendo servir de ponto de partida para uma análise mais elaborada dos mecanismos reacionais utilizando modelos explícitos para o solvente. O mecanismo de oxidação de catecóis – representado pelo substrato modelo, o 3,5-di-tercbutilcatecol (DTBC) – no sítio ativo do complexo R1 foi avaliado através de cálculos quanto-mecânicos. Embora não tenham sido obtidos resultados conclusivos acerca da cinética da reação, os aspectos estruturais das principais espécies envolvidas no ciclo catalítico foram analisados. / In this thesis the theoretical investigation of the hydrolytic cleavage mechanism of a phosphate diester, BDNPP [bis(2,4-dinitrophenyl)phosphate] in the active site of the dinuclear copper complex, labelled as R1, has been proposed. The metal complex was originally designed to mimic the active site structure as well the catalytic properties of catechol oxidase, revealing an interesting case of catalytic promiscuity in biomimetic systems. The mechanistic possibilities have been carefully evaluated through Density Functional Theory (DFT) calculations in gas phase and in aqueous solution using continuum solvation models with single point calculations within the Polarizable continuum model (PCM). Two reaction mechanisms have been proposed. The Mechanism 1 (Concerted) is a SN2 type mechanism which involves the direct attack of the µ-OH bridge between the two copper(II) ions towards the phosphorus center whereas, the Mechanism 2 (Associative) occurs through two successive proton transferences between the oxygen atom of the bridging hydroxo ligand and another oxygen atom of the phosphate model forming a stable pentacoordinate intermediate. There are two reactions paths for Mechanism 1 to release the DNPP (2,4-dinitrophenylphosphate) ion generated after the hydrolytic cleavage. The first reaction path (p1) involves a proton transfer immediately after the hydrolytic cleavage, being the proton transfer the rate-determining step, followed by the entry of two water molecules. The second reaction path (p2) comprises the entry of two water molecules just after the hydrolytic cleavage without any proton transfer, being the hydrolytic cleavage the rate limiting step. The most probable catalytic path occurs via Mechanism 1, following the second reaction path (p2) once it involves the lowest free energies activation barrier (ΔG‡ = 23.7 kcal mol-1, in aqueous solution). The experimental rate constant, Kobs is 1.7 × 10-5 s-1, indicating that the calculated value, (K1 = 2.6 × 10-5 s-1) is in a very good accordance with the experimental value. Kinetic Isotope Effect (KIE) analysis for the second reaction path (p2) within the Mechanism 1 has also been considered in order to understand the changes taking place in TS1-i (transition state of Mechanism 1) and perfectly characterize the mechanism here described. The solvent effect using explicit water molecules were evaluated in a preliminary fashion for one structure within the catalytic cycle of hydrolytic cleavage of phosphate ester, using the Monte Carlo method. The obtained results allows a detailed analysis of the water molecules organization around the complex, serving as a starting point for an more elaborated study of the reaction mechanisms by using explicit solvent models. The oxidation of catechols – represented herein by the model substrate, 3,5-di-tercbuthylcatechol (DTBC) – in the active site of the R1 complex were evaluated by using quantum-mechanical calculations. The results are not conclusive for the kinetic, but the structural aspects for the main species in the catalytic cycle were studied.