The Quantum chemical cluster approach has been shown to be quite powerful and efficient in the modeling of enzyme active sites and reaction mechanisms. In this thesis, the reaction mechanisms of several enzymes have been investigated using the hybrid density functional B3LYP. The enzymes studied include four dinuclear zinc enzymes, namely dihydroorotase, N-acyl-homoserine lactone hydrolase, RNase Z, and human renal dipeptidase, two trinuclear zinc enzymes, namely phospholipase C and nuclease P1, two tungstoenzymes, namely formaldehyde ferredoxin oxidoreductase and acetylene hydratase, aspartate α-decarboxylase, and mycolic acid cyclopropane synthase. The potential energy profiles for various mechanistic scenarios have been calculated and analyzed. The role of the metal ions as well as important active site residues has been discussed.   In the cluster approach, the effects of the parts of the enzyme that are not explicitly included in the model are taken into account using implicit solvation methods.   For all six zinc-dependent enzymes studied, the di-zinc bridging hydroxide has been shown to be capable of performing nucleophilic attack on the substrate. In addition, one, two, or even all three zinc ions participate in the stabilization of the negative charge in the transition states and intermediates, thereby lowering the barriers.   For the two tungstoenzymes, several different mechanistic scenarios have been considered to identify the energetically most feasible one. For both enzymes, new mechanisms are proposed.   Finally, the mechanism of mycolic acid cyclopropane synthase has been shown to be a direct methyl transfer to the substrate double bond, followed by proton transfer to the bicarbonate.   From the studies of these enzymes, we demonstrate that density functional calculations are able to solve mechanistic problems related to enzymatic reactions, and a wealth of new insight can be obtained.

Aquest treball teòric estudia l'acoblament magnètic en complexos bi- i trinuclears heterometàl·lics amb lligands pont oxamido, oxamato, ditiooxalato i anàlegs. Per calcular la seva estructura electrònica s'han usat mètodes multireferencials, en particular diferents variants del mètode DDCI, desenvolupat en el grup, i el mètode CASPT2. Per diferents sistemes binuclears coneguts de Cu(II) i Mn(II), l'acoblament magnètic i els mapes de densitat de spin calculats reprodueixen acuradament les dades experimentals. L'acoblament antiferromagnètic en aquests depèn de la transferència de càrrega del lligand al metall, lligada a l'electronegativitat dels àtoms coordinats. En els sistemes hipotètics de tipus Cu(II)-M(II)-Cu(II), on M=Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu i Zn, la magnitud de l'acoblament estimada depèn de l'electronegativitat del metall central, anant de feblement ferromagnètic pel Sc a moderadament antiferromagnètic pel Cu. Aquest treball aporta la interpretació microscòpica de l'acoblament en aquests sistemes, així com la validació i/o les limitacions dels mètodes de càlcul emprats. / This theoretical work examines the magnetic coupling in bi- and trinuclear heterometallic transition metal complexes with bridging ligands such as oxamido, oxamato, ditiooxalato and analogues. To calculate their electronic structure multireference methods have been used, including different variants of DDCI method, developed in our group, and CASPT2 method. For different Cu(II)-Mn(II) binuclear known systems, the magnetic couplings and spin density maps calculated accurately reproduce the experimental data. The antiferromagnetic coupling in these compounds depends on the charge transfer from ligand to metal, linked to the electronegativity of coordinated atoms. In the hypothetical systems of type Cu(II)-M(II)-Cu(II), where M = Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu and Zn, the magnitude of the estimated coupling depends on the electronegativity of the metal core, going from the weakly ferromagnetic for Sc to moderately antiferromagnetic for Cu. This work provides the microscopic interpretation of the coupling in these systems, as well as the validation and/or limitations of the computational methods used.

Neste trabalho foram realizadas as sínteses e caracterizações dos precursores (1) [Ru3O(CH3COO)6(CH3OH)3]CH3COO, (2) [Ru3O(CH3COO)6(CO)(CH3OH)2] (3) [Ru3O(CH3COO)6(4-acpy)2(H2O)]PF6, (4) [Ru3O(CH3COO)6(4-tbpy)2(H2O)]PF6 e dos complexos inéditos (5) [Ru3O(CH3COO)6(4-acpy)2(CO)], (6) [Ru3O(CH3COO)6(4-tbpy)2(CO)], (7) [Ru3O(CH3COO)6(4-acpy)2(NO)]PF6, (8) [Ru3O(CH3COO)6(4-tbpy)2(NO)]PF6. Os complexos foram caracterizados por espectroscopia na região do UV-Vis e do infravermelho, espectroscopia de ressonância magnética nuclear (RMN), voltametria cíclica e análise elementar. Por meio dos resultados obtidos nas técnicas de caracterização, foi possível confirmar a estrutura proposta inicialmente para os complexos e também para os precursores. Além disso, também foi possível observar a influência dos ligantes, -receptor e -doador na estrutura dos mesmos. Por meio da técnica de espectroscopia de infravermelho analisou-se principalmente estiramentos dos ligantes CO nos complexos 5 e 6 e do NO nos complexos 7 e 8. Nos estudos de RMN observou-se as características diamagnéticas dos complexos 5 e 6, e no caso dos complexos 7 e 8 foi possível confirmar que há uma forte interação entre o elétron desemparelhado na unidade [Ru3O]+ e do ligante NO0. Os ensaios eletroquímicos de voltametria cíclica mostraram a influência dos ligantes CO e NO na comunicação eletrônica da unidade [Ru3O].Os complexos com ligantes CO e NO foram irradiados com laser em 377 nm e 660 nm em soluções de acetonitrila e tampão fosfato pH 7,4. Estas irradiações foram acompanhadas por espectroscopia na região do UV-visível. No caso dos complexos 5 e 6, o aumento da banda na região de 900 nm indicou a formação do complexo, [Ru3O(CH3COO)6(L)2(S)], após a liberação do ligante monóxido de carbono (CO). A liberação de CO ocorreu predominantemente com irradiação em 377 nm na região do ultravioleta em pH fisiológico (solução aquosa de tampão fosfato, pH=7,4) e também em solução de acetonitrila. Para os complexos com ligantes NO, o perfil espectral obtido após fotólise indicou a formação de um complexo oxidado sem a coordenação do NO, [Ru3O(CH3COO)6(L)2(S)]+. / In this study it was performed the synthesis and characterization of the precursors (1) [Ru3O(CH3COO)6(CH3OH)3]CH3COO, (2) [Ru3O(CH3COO)6(CO)(CH3OH)2] (3) [Ru3O(CH3COO)6(4-acpy)2(H2O)]PF6 (4) [Ru3O(CH3COO)6(4-tbpy)2(H2O)]PF6 and the unpublished complexes (5) [Ru3O(CH3COO)6(4-acpy)2(CO)] (6) [Ru3O(CH3COO)6(4-tbpy)2(CO)] (7) [Ru3O(CH3COO)6(4-acpy)2(NO)]PF6 (8) [Ru3O(CH3COO)6(4-tbpy)2(NO)]PF6. The complexes were characterized by UV-Vis and infrared spectroscopy, nuclear magnetic resonance (NMR), cyclic voltametry, and elemental analysis. By means of the results obtained from the characterization, it was possible to confirm the initially proposed structure for both complexes and precursors. Furthermore, it was also possible to observe the influence of ligands, - receptor and the -donor in the structure of the complexes. By infrared spectroscopy it was verified primarily stretches of the CO and NO ligands in complexes 5,6 and 7,8 respectively. In NMR it was observed the diamagnetic character of complexes 5 and 6, and in the case of complexes 7 and 8 it was confirmed that there is a strong interaction between the unpaired electron in the [Ru3O]+ unit and the NO0 ligand. The cyclic voltammograms showed the influence of the CO and NO ligands on the electronic communication of the [Ru3O] unit. Complexes with ligands CO and NO were irradiated with laser at 377 nm and 660 nm in solutions of acetonitrile and phosphate buffer pH 7.4. The photolysis were accompanied by spectroscopy in the UV-visible region. In the case of complexes 5 and 6, the increase of the band in the region of 900 nm indicated the formation of the complex, [Ru3O(CH3COO)6(L)2(S)]+ produced after release of carbon monoxide (CO). The release of CO occurs predominantly with irradiation at 377 nm in the ultraviolet region at physiological pH (aqueous phosphate buffer solution, pH = 7.4) and in acetonitrile solution. For complexes with NO ligands, the spectral profile obtained after photolysis indicated the formation of an oxidized complex without coordination of NO, the [Ru3O(CH3COO)6(L)2(S)] + molecule.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-05-15T14:18:18Z No. of bitstreams: 1 nathaliamagalhaespaixao.pdf: 3549646 bytes, checksum: dfd913fd20520fb3cbfe42b45a3b6f5f (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-05-17T15:59:23Z (GMT) No. of bitstreams: 1 nathaliamagalhaespaixao.pdf: 3549646 bytes, checksum: dfd913fd20520fb3cbfe42b45a3b6f5f (MD5) / Made available in DSpace on 2017-05-17T15:59:23Z (GMT). No. of bitstreams: 1 nathaliamagalhaespaixao.pdf: 3549646 bytes, checksum: dfd913fd20520fb3cbfe42b45a3b6f5f (MD5) Previous issue date: 2017-02-20 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Câncer é um processo de crescimento e disseminação incontrolado de células e tem sido considerado como uma questão de saúde pública. Os compostos polinucleares de Platina (II) têm se mostrado muito promissores contra células cancerosas devido a interações mais rápidas e efetivas em comparação com os compostos mononucleares, como por exemplo, o complexo BBR3464. A partir disso, diversos estudos vêm sendo realizados com intuito de descrever os modos de interação de tais compostos. Este trabalho tem como objetivo fornecer um estudo teórico sistemático do complexo trinuclear de platina (II), AH78, através do uso de diferentes níveis de cálculo. Os compostos trinucleares de platina (II) estudados nesse trabalho não são capazes de formar ligações covalentes com o DNA, interagindo através da formação de grampos de fosfato, que são preferencialmente interações de hidrogênio e eletrostáticas. Dessa forma, este trabalho teve como motivação avaliar a interação dos complexos trinucleares de platina (II) não covalentes com o DNA por meio da formação de grampos de fosfato, analisadas através de modelos miméticos demonstrando presença de tais interações a partir de uma análise mais rápida e eficaz. Foram obtidas estruturas contendo uma fração de DNA que contém 6 pares de bases nitrogenadas e o complexo AH78, utilizando o método ONIOM, que comprovam a existência dos grampos de fosfato entre o complexo e o DNA. / Cancer is a process of uncontrolled growth and spread of cells and has now been considered a public health issue. Polynuclear Platinum (II) Complexes (PPCs) have shown very promising against cancer cells because of faster and more effective interactions compared to mononuclear compounds, such as the BBR3464 complex. From this, several studies have been carried out to describe the modes of interaction of such compounds. This work provides an extensive and systematic theoretical study of the platinum (II) trinuclear complex, AH78, using different base set functions for C, N and H atoms, including diffusive and polarization functions and different ECPs for platinum. The platinum (II) trinuclear compounds studied in this work are not able to form covalent bonds with DNA, interacting by the formation of phosphate bonds, which are preferably hydrogen type and electrostatic interactions. Thus, this work had the motivation to evaluate the interaction of non-covalent platinum (II) trinuclear complexes with DNA by means of the formation of phosphate clamps, analyzed using mimetic models, demonstrating that the presence of such interactions from a faster analysis is efficient. Structures containing a DNA fraction were obtained with six purine base pairs and AH78 complex using the ONIOM method, which demonstrate the existence of the phosphate clamps between the complex and the DNA.

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