Interactions of Metal Cations in Bioorganic Environment Computational Study Using Quantum Mechanics and Molecular Mechanics Tools Zdeněk Futera Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied by QM/MM computational technique. The whole re- action mechanism is divided into three phases - hydration of [RuII (η6 - benzene)(en)Cl]+ , consequent binding DNA and final intra-strand cross-link formation between two adjacent guanines. Free energy profiles of all reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex is described by DFT. For that purpose, special QM/MM software was developed to couple Gaussian and Amber programs. Calculated free energy barriers of Ru(II) hydration as well as DNA binding process are in good agreement with experimentally determined rate constants. Reaction pathway for cross-link formation was predicted that is feasible from both thermodynamical and kinetical point of view.

Les structures cristallographiques de macromolécules comme les protéines, obtenues par la biologie structurale sont des modèles statiques. Or, c'est la flexibilité et la dynamique de ces macromolécules qui sont généralement responsables de leurs fonctions. La simulation permet d'explorer cette flexibilité lors de différents phénomènes qui ont lieu dans ces systèmes : une réaction chimique, des interactions avec une petite molécule… Simuler de tels phénomènes est un défi car la dynamique moléculaire classique ne permet pas de les observer. Des algorithmes permettent d'accélérer l'échantillonnage des dynamiques pour lever cette limitation et de calculer les barrières d'activation pour de tels phénomènes. Simultanément, le choix du niveau de calcul est crucial car il faut concilier la taille importante des systèmes, la nature des interactions et les phénomènes électroniques impliqués. Dans ce travail, différentes méthodes, dont principalement la métadynamique soit au niveau classique ou quantique, ou encore en combinant les deux niveaux quantique/classique, seront utilisées pour modéliser quatre processus complexes : des changements de conformations d'une protéine, des interactions entre métalloprotéine et inhibiteur, des réactions en solution et dans une enzyme. / Crystallographic structures of macromolecules, such as proteins, obtained by structural biology are static models. However, flexibility and dynamics of macromolecules are generally responsible for their functions. Modeling allows us to explore this flexibility in different phenomena that take place in these systems: a chemical reaction, interaction with a small molecule... Modeling such phenomena is a challenge because they cannot be observed by classical molecular dynamics. Algorithms can accelerate sampling of dynamics to simulate these events and calculate their activation barriers. Simultaneously, the choice of the level of calculation is crucial because it must merge with the size of the systems, the nature of interactions and the electronic phenomena involved.In this thesis, some methods, mainly metadynamics at classical level, quantum or the hybrid quantum/classical level, will be used to model four complex processes: conformational changes of proteins, metalloprotein/inhibitor interactions, reactivity in solution and enzymatic reactivity.

Neste trabalho estudamos o espectro de absorção da clorofila d, incluindo os efeitos do solvente metanol, utilizando a Teoria do Funcional da Densidade Dependente do Tempo em combinação com o método s-QM/MM. Diferentes abordagens para a descrição do meio solvente, que vão desde o modelo contínuo polarizável até a inclusão de moléculas explícitas do solvente, são utilizadas. Observamos que a inclusão do solvente desloca o espectro, em relação ao calculado em vácuo, para o vermelho. A inclusão de 20 moléculas explícitas de metanol e 880 representadas como as cargas pontuais do seus átomos para a descrição do meio solvente foi a que melhor concordou com os valores experimentais. Mediante cálculos de mecânica quântica obtivemos para o complexo composto por a molécula de clorofila d e apenas uma de metanol explícita um deslocamento do átomo de magnésio da clorofila d em relação ao anel de 0,31 Å. Mediante a analise da função de distribuição radial de pares obtida da simulação clássica comprovamos que esse átomo de magnésio é penta-coordenado. Além disso, é usada uma estrutura simplificada da clorofila d baseado na localização dos orbitais moleculares participantes das transições eletrônicas com o objetivo de diminuir o custo computacional dos cálculos de mecânica quântica. Os espectros calculados para a clorofila d não apresentaram diferenças significativas com os calculados para a simplificação proposta. Como complementação o espectro Raman da clorofila d isolada é calculado mediante DFT e alguns dos modos normais são caracterizados. / In this work we study the absorption spectrum of chlorophyll d, including the effects of the solvent methanol, using the Time Dependent Density Functional Theory in combination with the method s-QM/MM. Different approaches for the description of the solvent medium, ranging from the polarizable continuum model to the inclusion of explicit solvent molecules, are used. We note that the inclusion of solvent shifts the spectrum, relative to that calculated in vacuum, to the red side of the spectrum. The inclusion of 20 explicit molecules of methanol and 880 represented as point charges of their atoms for the description of the solvent medium was the one that best agreed with the experimental values. By quantum mechanics calculations we obtained for the complex composed of the molecule of chlorophyll d and only one explicit methanol molecule a displacement of the magnesium atom of chlorophyll d in relation to the ring of 0,31 Å. By means of the analysis of the radial distribution function obtained from the classic simulation we can see that this atom of magnesium is penta-coordinated. In addition, a simplified structure of chlorophyll d is used based on the location of the molecular orbitals involved in the electronic transitions in order to reduce the computational cost of quantum mechanics calculations. The spectra calculated for chlorophyll d did not show significant differences with those calculated for the proposed simplification. As a complement the Raman spectrum of isolated chlorophyll d is calculated by DFT and some of the normal modes are characterized.

Made available in DSpace on 2016-03-15T19:35:53Z (GMT). No. of bitstreams: 1 Ray Fernando Hidalgo Ramirez.pdf: 3985319 bytes, checksum: 0a36b0e596cb2c3f1eadaccfa8f843ee (MD5) Previous issue date: 2015-06-17 / Universidade Presbiteriana Mackenzie / Solar flares radio emissions provide detailed information on the energy release, particle acceleration, heating processes and plasma conditions at the sites where the radiation is generated. This study focuses in radio emission from millimeter, sub-millimeter and another complementary wavelengths obtained by recent observations that might improve the understanding of processes from the low chromosphere to the corona. Here we study a GOES class X1.7 flare on January 27, 2012 detected by the Solar Sub-millimeter Telescope (SST) at 212 and 405 GHz, and by the solar radio polarimeters (POEMAS) at 45 and 90 GHz. LASCO C2 coronagraph observed a coronal mass ejection (CME) with possible physical connection with phenomena observed at radio-frequencies, including changes in polarization degree (45 and 90 GHz) and enhancements of scintillation index (212 and 405 GHz). The complementary radio observations were obtained by the Radio Solar Telescopes Network (RSTN) at the single frequencies 0.2, 0.4, 0.6, 1.4, 2.7, 4.9, 8.8 and 15.4 GHz and at the 25 - 180 MHz band, and by the Green Bank Solar Radio Burst Spectrometer (GBSRBS) at the 100 - 300 MHz and 300 - 1200 MHz bands. The solar flare exhibits a complex time structure at microwaves consisting of three major enhancements. Type III-like metric and decametric bursts were accompanied by small polarized burst at 45 and 90 GHz with polarization degrees of 0.09 and 0.12, suggesting changes in the magnetic field strength the order of 700 and 2000 G, respectively. SST detected one impulsive burst and significant 10% enhancements of scintillation index intermittently throughout the event. The CME launch time inferred by back extrapolation of the LASCO coronagraph observations to the solar limb coincides approximately in time to the changes in polarization degree, suggesting that CME might be a result of a magnetic transient causing an instability generating the subsequent impulsive structures. / As emissões em rádio das explosões solares provém informações detalhadas dos processos de liberação de energia, aceleração de partículas, aquecimento e condições do plasma na região onde a radiação é gerada. Este estudo concentra-se em rádio emissões nos comprimentos de onda milimétricos, sub-milimétricos e outras frequências complementares obtidas por observações recentes que podem melhorar o entendimento dos processos na baixa cromosfera até a coroa. Foi estudada uma explosão solar classe GOES X1.7 ocorrida no dia 27 de janeiro de 2012, detectada pelo Telescópio Solar Sub-milimétrico (SST) em 212 e 405 GHz e pelos rádio polarímetros solares em 45 e 90 GHz. Uma ejeção de massa coronal (CME) foi observada pelo coronógrafo C2 de LASCO com possível conexão física com os fenômenos observados em rádio frequências, incluindo mudanças no grau de polarização (45 e 90 GHz) e aumentos no índice de cintilação (212 e 405 GHz). As rádio observações complementares foram obtidas em frequências distintas, pela Rede de Rádio Telescópios Solares (RSTN), de 0,2; 0,4; 0,6; 1,4; 2,7; 4,9; 8,8 e 15,4 GHz e nas faixas de 25 - 180 MHz, e pelo Rádio Espectrômetro Solar Green Bank (GBSRBS) nas faixas de 100 - 300 MHz e 300 - 1200 MHz. A explosão solar apresenta uma estrutura temporal complexa em micro-ondas composta por três aumentos característicos. Explosões métricas e decamétricas tipo III foram acompanhadas por pequenas explosões com polarização em 45 e 90 GHz com graus de polarização de 0,09 e 0,12, sugerindo variações de campo magnético da ordem de 700 e 2000 G, respectivamente. O SST detectou uma explosão impulsiva e aumentos significativos de 10% no índice de cintilação de forma intermitente durante todo o evento. O tempo de lançamento da CME inferido por extrapolação das observações do coronógrafo LASCO ao limbo solar coincide aproximadamente com o instante do excesso de emissão e mudança do grau de polarização em 45 e 90 GHz, sugerindo que a CME tenha resultado de um transiente magnético ocasionando uma instabilidade que gerou as estruturas impulsivas subsequentes.

As transições eletrônicas que apresenta as energias mais baixas no retinal e em quatro retinais sintéticos foram analisadas em dois diferentes ambientes: no vácuo e ligados à proteína bacterioopsina por uma base de Schiff protonada, utilizando diversos métodos de química teórica. Os resultados aqui apresentados fornecem indicativos de que três estados eletrônicos estão envolvidos na formação da primeira banda de absorção dos aldeídos, enquanto que, no caso dos compostos ligados à proteína apenas dois estados estariam envolvidos. As análises discutidas neste trabalho também sugerem uma possível explicação para o envolvimento de dois estados eletrônicos excitados no processo de fotoisomerização do retinal ligado à bacterioopsina. / Low-lying electronic transitions of retinal and of four synthetic retinals were analyzed in two different environments: in vacuum and linked to bacterioopsin through a protonated Schiff base, employing several methods of theoretical chemistry. The results here reported suggest that the first absorption band of the aldehydes involves three electronic states, while for the case of protein linked compounds, two states would be embraced. Our discussions also provided a possible explanation about the involvement of two electronic excited states in the photoisomerization process of retinal linked to bacterioopsin.

Absorção e Emissão de radiação eletromagnética por moléculas na região do UV-Vis fornece informações sobre os estados eletrônicos excitados, sendo propriedades de grande interesse devido a sua relação com processos biológicos, bem como suas possíveis aplicações em diagnósticos e tecnologia. Essas propriedades são sensíveis ao meio em que as moléculas se encontram, tornando-se assim natural a busca por métodos teóricos que possibilitam descrever essas interações. Neste trabalho, nós usamos a metodologia Sequential-Quantum Mechanics/Molecular Mechanics para estudar o espectro de absorção e de emissão de moléculas de relevância biológica, quando em solução. Simulações clássicas Monte Carlo foram usadas pra construir uma configuração eletrostática média do líquido para posterior cálculo das propriedades, feito através dos métodos multiconfiguracionais CASSCF e CASPT2. Cuidados especiais foram tomados para incluir a polarização eletrônica que o soluto sofre devido à presença do solvente. Nossa contribuição é a adaptação do método do Gradiente de Energia Livre para permitir a obtenção de geometrias de estados excitados do soluto em solução. A técnica foi implementada em um programa e aplicada com sucesso nos sistemas estudados. As perspectivas agora se abrem para a obtenção de intersecções cônicas em meio solvente, permitindo assim o estudo de decaimentos não-radiativos em sistemas solvatados. / Absorption and emission of electromagnetic radiation by molecules in the UV-Vis region yields information about the electronic excited states, being properties of great interest due its relation with biological process, as well as its possible applications in diagnostics and technology. These properties are sensible to the environment in which the molecules are, making natural the search for theoretical methods that describe these interactions. In this work, we have used the Sequential-Quantum Mechanics/Molecular Mechanics methodology to study the spectrum of absorption and emission of molecules of biological relevance, when in solution. Classical Monte Carlo simulations were carried out to construct an average solvent electrostatic configuration and used to represent the liquid in posterior quantum mechanics calculation of the properties, performed by using the multiconfigurational methods CASSCF and CASPT2. Special cares were taken to include the electronic polarization of the solute due the solvent. Our contribution is the adaptation of the Free Energy Gradient method to allow the determination of the solute excited states geometries in solution. The method was implemented in a computer program and successfully applied in the systems studied. The perspectives are now open to the calculation of conical intersection in solvent environment, enabling the study of nonradioactive decays in solvated systems.

La thèse porte sur l’étude des 2 premières enzymes de la voie du MEP: la DXS et DXR. La voie du MEP conduit à la biosynthèse des isoprénoïdes chez la plupart des bactéries, dont des pathogènes. Etant absente chez l’homme, les enzymes de cette voie cible idéale pour la recherche de nouveaux antimicrobiens. L’objectif principal était d’améliorer le développement de nouveaux antimicrobiens. Nous avons utilisé des outils computationnels : méthodes de docking et de mécanique moléculaire couplée à la méthode MM/PBSA. Nous avons identifié les résidus contribuant significativement à la fixation d’un ligand dans le site actif de la DXR. Ces résultats ont été utilisés lors de la conception de nouveaux candidats inhibiteurs de type bisubstrat, biligand et difluoro phosphonate, dont 2 ont pu être synthétisés. Nous avons également développé une méthode de synthèse donnant accès au L- et D-GAP énantiomeriquement purs, dans le but d’étudier l’énantiospécificité de la DXS face à son substrat D-GAP. / This thesis concerns the study of the 2 first enzymes of the MEP pathway: DXS and DXR. The MEP pathway permits the biosynthesis of isoprénoïdes in most bacteria, including pathogenic one. As it is not present in human, enzymes of MEP pathway are effective targets in the research of new antimicrobial drugs. The objective was to advance the development of new antimicrobiotic compounds. We used computational tools: molecular docking and molecular dynamics simulations coupled with an MM/PBSA approach. We were able to identify residues that contribute significantly to the ligand binding in the DXR active site. These results were used to guide the conception of new inhibitor models, such as bisubstrates, biligands and α,α-difluoro phosphonates, two of which were synthetized. We also developed a synthesis method to obtain L- and D-GAP as enantiomerically pure molecules. The goal was to study the enantiospecificity of DXS to its substrate, D-GAP.

La bioluminescence est un processus complexe dans lequel la réaction chimique d'un substrat, catalysée par une protéine, entraîne l'apparition d'une émission de lumière dans le spectre visible. Dans le cas des lucioles, un insecte émettant dans le domaine du jaune-vert, le substrat se nomme luciférine et la protéine luciférase. Cependant, la taille et la complexité de ce système chimique limite sa compréhension, notamment celle du mécanisme réactionnel.L'apport de la chimie théorique dans ce domaine est essentiel et a prouvé son utilité dans de nombreux cas. L'utilisation de la méthode QM/MM, méthode hybride couplant la mécanique quantique et la mécanique moléculaire permet de modéliser et d'étudier ces systèmes biologiques.Cette thèse se focalise sur deux approches différentes de l'étude de la bioluminescence chez les lucioles. La première consiste à étudier l'effet de certaines modifications chimiques sur la couleur de la bioluminescence. On s'intéresse plus particulièrement à un analogue de la luciférine et à certaines luciférases issues d'autres systèmes bioluminescents. Par cette étude on cherche à rationaliser et à prédire l'effet ainsi que l’impact de ces changements sur l’émission. Le deuxième sujet explore deux étapes du mécanisme réactionnel de la bioluminescence: d'une part, la coordination du dioxygène sur un intermédiaire de la réaction, une étape encore non étudiée et d'autre part la réaction de tautomérisation dans l'état excité et au sein de la protéine entre deux formes émissives possibles de la luciférine / The bioluminescence is a complex process that involves the reaction of a substrate, catalysed by an enzyme that sheds light in the visible spectra. In fireflies, the light emitted has a yellow-green tone thanks to the interaction between the substrate luciferin and the protein luciferase. However the size and the complexity of the system prevent its comprehension especially when dealing with the reaction mechanism.The use of computational chemistry is key to understand and improve the comprehension of the bioluminescence. The hybrid QM/MM method that combines quantum mechanics with molecular mechanics is a great tool to model and study bioluminescent systems.This thesis deals with two different approaches of the bioluminescence in fireflies. The first one is related to the study of chemical modifications that tune the emission colour. We will discuss about one analogue of the luciferin and on new luciferases from others bioluminescent species. The goals of this study are to rationalise and predict both the effect and the impact of these modifications on the emission. The second subject deals with two different steps of the bioluminescent mechanism. The first one discusses the binding of the dioxygen to the bioluminescent intermediate, which was so far unstudied and the second one about the tautomerization in the excited state and in the protein of two possible emissive forms of the luciferin

L’obtention, dans des conditions douces, sélectives et de chimie durable de molécules ciblées est aujourd’hui un enjeu majeur. Les métalloenzymesartificielles représentent une voie d’investigation importante, car en jouant, par exemple, sur la seconde sphère de coordination,il est possible de modifier fortement la réactivité de ces systèmes bio-inspirés. Le développement de cette chimie suppose une connaissanceapprofondie des différentes étapes du mécanisme de la réaction envisagée. Pour cela, la chimie théorique est essentielle à la rationalisation dela réactivité chimique mais elle souffre encore de nombreuses insuffisances pour les systèmes que nous nous proposons d’étudier.Dans ce travail, nous avons choisi d’étudier la superoxyde réductase, enzyme détoxifiante du radical superoxyde. Si de nombreuses expérimentalessont disponibles détaillant certains intermédiaires, le mécanisme précis est peu documenté. Le but a été de mettre en place uneméthodologie complète allant du développement de paramètres MM spécifiques à l’étude de la réactivité par métadynamiques QM/MM.Le développement de paramètres MM pour le site actif à fer a permis son étude en dynamique MM donnant des informations sur la conformationsdu squelette peptidique ainsi que l’interaction avec les molécules de solvant. De part la nature du fer, une description QM du site actifà été nécessaire via l’utilisation de DFT hybride. Les métadynamiques QM/MM ont permis quant à elles d’explorer les chemins réactionnelset de caractériser les espèces ainsi formées et les énergies d’activations.Cette méthodologie a permis la compréhension en premier lieu de la réactivité native de la forme sauvage et elle a aussi permis d’explorer lesréactivités nouvelles des mutations de la SOR permettant ainsi de définir le rôle crucial de la seconde sphère de coordination. / Obtaining targeted molecules under gentle, selective and sustainable conditions is still a major challenge. Artificial metalloenzymes are animportant line of enquiry, because by playing, for example, with the second sphere of coordination, it is possible to strongly modify thereactivity of these bio-inspired systems. The development of this chemistry presupposes a thorough knowledge of the different stages of themechanism of the reaction under study. For this reason, theoretical chemistry is essential to rationalize chemical reactivity, but it still suffersfrom many shortcomings for the systems we propose to study.In this work, we study the superoxide reductase, a detoxifying enzyme of the superoxide radical. While many experiments are available detailingsome intermediates, the precise mechanism is not well documented. The aim was to implement a complete methodology ranging from thedevelopment of specific MM parameters to the study of reactivity by QM/MM metadynamics.The development of MM parameters for the iron active site allowed its study by MM dynamics giving informations on the conformation ofthe peptide backbone as well as on the interaction with solvent molecules. Due to the nature of the iron, a QM description of the active sitewas required using hybrid DFT. QM/MM metadynamics have allowed us to explore reaction pathways and to characterize the compoundsformed to obtain the needed activation energies. This methodology made it possible to understand the native reactivity of the wild form ofthe SOR, but also to explore the new reactivity of the mutations of the SOR and thus to define the crucial role of the second coordination sphere.

Nous avons étudié l'effet des rayons cosmiques dans les détecteurs en utilisant un bolomètre de germanium composite NTD à basse température, et une source de particules alpha comme source générique d'impulsions. Nous avons caractérisé ce bolomètre en constatant que la forme de son impulsion était due à la combinaison de sa réponse impulsionnelle (la somme de deux exponentielles doubles), et des effets liés à la position découlant de la thermalisation des phonons balistiques en phonons thermiques dans son absorbeur. Nous avons établi un schéma décrivant la forme de l'impulsion dans ce bolomètre en comparant une impulsion mathématique générique à une seconde description basée sur la physique thermique. Nous constatons que la thermalisation des phonons balistiques, suivie de la diffusion thermique, jouent un rôle important dans la forme de l'impulsion, en parallèle avec le couplage électrothermique et les effets électriques dépendant de la température. Nous avons modélisé les impulsions en observant que leur comportement peut être reproduit en tenant compte de la réflexion de phonons balistiques sur le bord de l’absorbeur, avec un couplage thermique fort au capteur central du bolomètre. Compte tenu de ces résultats, nous étudions également les effets des rayons cosmiques sur l’instrument Athena X-Ray Integral Field Unit (X-IFU), en produisant des timelines simulées et en testant la hausse de la valeur moyenne de la température (RMS) sur la plaquette du détecteur. Nous montrons que le flux thermique attendu des rayons cosmiques est au même ordre de grandeur que le maximum autorisé ΔTRMS ce qui constitue une menace sur le budget de la résolution énergétique de l'instrument. / We have studied the effect of cosmic rays in detectors using a composite NTD germanium bolometer at low temperatures and an alpha particle source as a generic source of pulses. We have characterised this bolometer, finding that its pulse shape is due to a combination of its impulse response function (the sum of two double exponentials), and position-dependent effects arising from thermalisation of ballistic phonons into thermal phonons in its absorber. We have derived a scheme for describing the pulse shape in this bolometer, comparing a generic mathematical pulse shape with a second description based on thermal physics. We find that ballistic phonon thermalisation, followed by thermal diffusion, play a significant role in the pulse shape, along with electro-thermal coupling and temperature-dependent electrical effects. We have modelled the pulses, finding that their behaviour can be reproduced accounting for ballistic phonon reflection off the absorber border, with a strong thermal coupling to the bolometer’s central sensor. With these findings, we also investigate the effects of cosmic rays on the Athena X-Ray Integral Field Unit (X-IFU), producing simulated timelines and testing the average RMS temperature increase on the detector wafer, showing that the expected cosmic ray thermal flux is within the same order of magnitudeas the maximum allowed ΔTRMS, posing a threat to the instrument’s energy resolution budget.