This thesis encloses quantum chemical calculations performed in the framework of density functional response theory for evaluating electron paramagnetic resonance (EPR) spin Hamiltonian parameters of various spin-labels in different environments. These parameters are the well known electronic g-tensor and the nitrogen hyperfine coupling constants, which are extensively explored in this work for various systems. A special attention was devoted to the relationships that form between the structural and spectroscopic properties that can be accounted for as an environmental inuence. Such environmental effects were addressed either within a fully quantum mechanical formalism, involving simplified model structures that still capture the physical properties of the extended system, or by employing a quantum mechanics/molecular mechanics (QM/MM) approach. The latter implies that the nitroxide spin label is treated quantum mechanically, while the environment is treated in a classical discrete manner, with appropriate force fields employed for its description. The state-of- the art techniques employed in this work allow for an optimum accounting of the environmental effects that play an important role for the behaviour of EPR properties of nitroxides spin labels. One achievement presented in this thesis includes the first theoretical con_rmation of an empirical assumption that is usually made for inter-molecular distance measurement experiments in deoxyribonucleic acid (DNA), involving pulsed electron-electron double resonance (PELDOR) and site-directed spin labeling (SDSL) techniques. This refers to the fact that the EPR parameters of the spin-labels are not affected by their interaction with the nucleobases from which DNA is constituted. Another important result presented deals with the inuence of a supramolecular complex on the EPR properties of an encapsulated nitroxide spin-label. The enclusion complex affects the hydrogen bonding topology that forms around the R2NO moiety of the nitroxide. This, on the other hand has a major impact on its structure which further on governs the magnitude of the spectroscopic properties. The projects and results presented in this thesis offer an example of successful usage of modern quantum chemistry techniques for the investigation of EPR parameters of spin-labels in complex systems. / <p>QC 20130318</p>

Computational modelling of chemical systems is most easily carried out in the vacuum for single molecules. Accounting for environmental effects accurately in quantum chemical calculations, however, is often necessary for computational predictions of chemical systems to have any relevance to experiment. This PhD thesis focuses on accounting for environmental effects in quantum chemical calculations by quantum mechanics/ molecular mechanics (QM/MM) approaches, taking on diverse examples from the solid state, the liquid phase and the protein environment. The methods are applied to compute a variety of properties from transition metal NMR properties of molecular crystals and enzymes, via conformational properties of zwitterions in aqueous solution, to an intramolecular amidation reaction in peptides. Chapter 3 concerns QM/MM calculations of molecular properties in the solid state, both molecular crystals and metalloenzymes, with a focus on transition metal chemical shift and EFG properties. We demonstrate that solid-state effects on such properties in molecular crystals can be accounted for by a simple general black-box QM/MM approach. We also describe preliminary QM/MM calculations of 51V anisotropic NMR properties for a vanadium-dependent enzyme. In Chapter 4 the focus is on solvent effects on the conformational preference of a small zwitterionic molecule, 3F-γ-aminobutyric acid (3F-GABA), calculated using QM/MM molecular dynamics simulations. NMR spin-spin coupling constants in solution are also calculated. Our simulations highlight the difficulty of accounting for solvation effects well enough to achieve agreement with experimental observations. Chapter 5 concerns the reaction mechanism of an intramolecular amidation reaction in a bacterial peptide, predicted by QM/MM calculations. We predict a reaction mechanism that accounts well for the experimental observations both for the wild-type and mutants. We demonstrate that environmental effects can often be satisfactorily accounted for by QM/MM approaches, thus helping to bridge the gap between theory and experiment.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第21593号 / 理博第4500号 / 新制||理||1646(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 林 重彦, 教授 谷村 吉隆, 教授 寺嶋 正秀 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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<p dir="ltr">Plant and algae-based biofuels offer a compelling green energy solution, but the utility of biological photosynthesis is limited by inefficiency in energy production. Without the connection between the protein structure and optical spectra, it is challenging to modify optical properties for improving energy production. Chlorophyll proteins (CPs) are the primary work-horses of biological photosynthesis that absorb and transfer solar energy to chemically active reaction centers and control the chemical energy storage process. While the CP structures are well-known, predicting their optical and electronic properties remains a serious challenge. There are computational complications for treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. In this work, we aim to address some prominent issues with structure-based optical spectra predictions and the limitations in applying the Frenkel exciton model.</p>

ealizaram-se cálculos ab initio e semi-empíricos em 5-hidrotriptofano (5-OH-trp), 7-aza-triptofano (7-aza-trp) e triptofano (trp), determinando as superfícies de energia potencial (SEP) do estado fundamental (EF) e do primeiro estado excitado (1EE), em função dos ângulos X IND. 1 e X IND. 2, medidos nos diedros N-C IND.alfa-C IND.beta-C IND.gama e C IND.alfa-C IND.beta-C IND.gama- C IND.delta2, respectivamente. Esses compostos foram estudados nos estados de protonação zwitteriônico, neutro e aniônico. A SEP do EF na forma zwitteriônica fo obtida pelo método semi-empírico AM1 e utilizada como referência para os cálculos ab initio. Os cálculos de 1EE foram feitos utilizando o método de Interação de Configurações com excitações simples (ICS) e orbitais internos congelados. As energias de transição entre o EF e o 1EE após as otimizações foram obtidas pelo método semi-empírico INDO/S-CIS, permitindo a obtenção dos espectros teóricos de absorção ótica, pelas energias de transição das geometrias otimizadas no EF, e de fluorescência de estado estacionário, pelas energias de transição das geometrias otimizadas no 1EE. Medidas experimentais dos espectros de absorção ótica e de fluorescência de estado estacionário e resolvida no tempo foram realizadas com o 5-OH-trp e o 7-aza-trp em solução tampão fosfato, pH 7,4. Os decaimentos fluorescentes ajustados a mais de uma exponencial foram estudados em termos das populações relativas de Boltzmann nos EF e 1EE. As taxas do decaimento não-radiativo de transferência de elétrons no 1EE foram obtidas pela implementação computacional da Teoria de Marcus e do Método da Expansão de Perturbação Renormalizada (EPR). Além disso, otimizações de estruturas de estados de transição (ET) na SEP dos 1EE foram realizadas pelo Método Sunchronous Transiti-Guided Quasi-Newton e pelo algoritmo de Berny modificado. Para aproximar as condições experimentais, foram ) realizadas simulações por dinâmica molecular (DM) usando o método híbrido QM/MM no EF do 5-OH-trp na forma zwitteriônica, na presença do solvente aquoso representado explicitamente. Os resultados obtidos dos cálculos ab initio foram usados como referência para o início dessas simulações. As conformações visitadas no EF, os espectros teóricos de absorção ótica e as camadas de solvatação do solvente aquoso em torno do reagente são discutidas. / Semi-empirical and ab-initio calculations were performed on 5-hydroxytryptophan (5-OH-trp), 7-aza-tryptophan (7-aza-trp) and tryptophan (trp). The potential energy surface (PES) of the ground state (GS) and the lowest exited state (1ES) was determined as a function X IND. 1 e X IND. 2 angles corresponding to the dihedrals N-C IND.alfa-C IND.beta-C IND.gama e C IND.alfa-C IND.beta-C IND.gama- C IND.delta2, respectively. The compounds were studied in the zwitterionic, neutral and anionic states. The PES of the GS was obtained using the AM1 semi-empirical method and was used as a reference for the ab-initio calculations. The configuration interaction method with single excitations (CIS) was used for the calculations of the 1ES with frozen internal orbitals. After geometry optimization of GS, the transition energies to 1ES were obtained by INDO/S-CIS, giving the theoretical optical absorption spectrum. Similarly, following the geometry optimization of 1ES, the transition energies to GS were determined, giving the fluorescence emission spectrum. Experimental results were obtained for optical absorption and fluorescence spectra of 5-OH-trp and 7-aza-trp in phosphate buffer solution, pH 7.4. The fluorescence decay of the compounds was also examined. Decay profiles fitted to multiexponential function were analyzed in terms of Boltzmann relative populations in the GS and 1ES. The non-radioactive electron transfer rates in the excited state were obtained by computational implementation of the Marcus Theory with renormalized perturbation expansion method (RPE). In this study, optimizations of the transition states in the PES of the ground and lower excited states were performed by the Synchronous Transit-Guided Quasi-Newton method and the Berny algorithm modified. For further comparison with experimental conditions, molecular dynamic simulations for the zwitterionic 5-OH-trp were performed using the hybrid QM/MM method with explicit representation of the aqueous solvent. To start the simulations the results from ab-initio calculations were used. The conformations for the GS, the theoretical absorption spectrum and the solvation layers were compared to the experimental results

ealizaram-se cálculos ab initio e semi-empíricos em 5-hidrotriptofano (5-OH-trp), 7-aza-triptofano (7-aza-trp) e triptofano (trp), determinando as superfícies de energia potencial (SEP) do estado fundamental (EF) e do primeiro estado excitado (1EE), em função dos ângulos X IND. 1 e X IND. 2, medidos nos diedros N-C IND.alfa-C IND.beta-C IND.gama e C IND.alfa-C IND.beta-C IND.gama- C IND.delta2, respectivamente. Esses compostos foram estudados nos estados de protonação zwitteriônico, neutro e aniônico. A SEP do EF na forma zwitteriônica fo obtida pelo método semi-empírico AM1 e utilizada como referência para os cálculos ab initio. Os cálculos de 1EE foram feitos utilizando o método de Interação de Configurações com excitações simples (ICS) e orbitais internos congelados. As energias de transição entre o EF e o 1EE após as otimizações foram obtidas pelo método semi-empírico INDO/S-CIS, permitindo a obtenção dos espectros teóricos de absorção ótica, pelas energias de transição das geometrias otimizadas no EF, e de fluorescência de estado estacionário, pelas energias de transição das geometrias otimizadas no 1EE. Medidas experimentais dos espectros de absorção ótica e de fluorescência de estado estacionário e resolvida no tempo foram realizadas com o 5-OH-trp e o 7-aza-trp em solução tampão fosfato, pH 7,4. Os decaimentos fluorescentes ajustados a mais de uma exponencial foram estudados em termos das populações relativas de Boltzmann nos EF e 1EE. As taxas do decaimento não-radiativo de transferência de elétrons no 1EE foram obtidas pela implementação computacional da Teoria de Marcus e do Método da Expansão de Perturbação Renormalizada (EPR). Além disso, otimizações de estruturas de estados de transição (ET) na SEP dos 1EE foram realizadas pelo Método Sunchronous Transiti-Guided Quasi-Newton e pelo algoritmo de Berny modificado. Para aproximar as condições experimentais, foram ) realizadas simulações por dinâmica molecular (DM) usando o método híbrido QM/MM no EF do 5-OH-trp na forma zwitteriônica, na presença do solvente aquoso representado explicitamente. Os resultados obtidos dos cálculos ab initio foram usados como referência para o início dessas simulações. As conformações visitadas no EF, os espectros teóricos de absorção ótica e as camadas de solvatação do solvente aquoso em torno do reagente são discutidas. / Semi-empirical and ab-initio calculations were performed on 5-hydroxytryptophan (5-OH-trp), 7-aza-tryptophan (7-aza-trp) and tryptophan (trp). The potential energy surface (PES) of the ground state (GS) and the lowest exited state (1ES) was determined as a function X IND. 1 e X IND. 2 angles corresponding to the dihedrals N-C IND.alfa-C IND.beta-C IND.gama e C IND.alfa-C IND.beta-C IND.gama- C IND.delta2, respectively. The compounds were studied in the zwitterionic, neutral and anionic states. The PES of the GS was obtained using the AM1 semi-empirical method and was used as a reference for the ab-initio calculations. The configuration interaction method with single excitations (CIS) was used for the calculations of the 1ES with frozen internal orbitals. After geometry optimization of GS, the transition energies to 1ES were obtained by INDO/S-CIS, giving the theoretical optical absorption spectrum. Similarly, following the geometry optimization of 1ES, the transition energies to GS were determined, giving the fluorescence emission spectrum. Experimental results were obtained for optical absorption and fluorescence spectra of 5-OH-trp and 7-aza-trp in phosphate buffer solution, pH 7.4. The fluorescence decay of the compounds was also examined. Decay profiles fitted to multiexponential function were analyzed in terms of Boltzmann relative populations in the GS and 1ES. The non-radioactive electron transfer rates in the excited state were obtained by computational implementation of the Marcus Theory with renormalized perturbation expansion method (RPE). In this study, optimizations of the transition states in the PES of the ground and lower excited states were performed by the Synchronous Transit-Guided Quasi-Newton method and the Berny algorithm modified. For further comparison with experimental conditions, molecular dynamic simulations for the zwitterionic 5-OH-trp were performed using the hybrid QM/MM method with explicit representation of the aqueous solvent. To start the simulations the results from ab-initio calculations were used. The conformations for the GS, the theoretical absorption spectrum and the solvation layers were compared to the experimental results

Les méthodes hybrides alliant la mécanique quantique et la mécanique moléculaire (QM/MM) sont des outils adéquats pour traiter des systèmes biologiques. Les phénomènes électroniques souvent étudiés sur des petites molécules ont, dès lors pu être envisagés dans des environnements macromoléculaires. Ce travail explore trois phénomènes électroniques en présence d'un environnement protéique: l'absorption, la capture électronique et les ionisations de coeur. Nous avons employé les derniers développements de la méthode QM/MM {Local Self-Consistent Field} (LSCF) pour traiter la jonction covalente entre la partie QM et la partie MM ainsi que le couplage QM/MM avec le PCM. En premier lieu, nous nous sommes focalisés sur les spectres d'absorption de chromophores présents dans des macromolécules. Nous avons mis au point un couplage entre les méthodes LSCF/MM et PCM pour prendre en compte la polarisation électronique de l'environnement suite à l'absorption d'un photon par le chromophore. Ce modèle, le LSCF/MM\string:ERS, a été testé et validé sur le spectre d'absorption du complexe de squaraine-tétralactame. Une étude plus poussée a ensuite été réalisée sur une protéine fluorescente en décomposant la longueur d'onde d'absorption maximale en trois contributions physiques. Les effets de la substitution du chromophore ont aussi été évalués. Dans une seconde partie, nous avons étudié la capture électronique par un cyclotide contenant trois ponts disulfures, qui, après irradiation, forment des demi-liaisons caractéristiques (2c-3e). La dernière partie est consacrée à la validation de l'approche de la projection asymptotique. Elle a été réalisée dans le cadre d'une étude sur les ionisations de coeur d'un ensemble de molécules pour, par la suite, étudier les ionisations de coeur de la glycine présentes dans des systèmes de plus en plus complexes jusqu'à la Sérum-Albumine Humaine. / Hybrid methods that combine quantum mechanics and molecular mechanics (QM/MM) provide a near-ideal treatment of biological system reactivity and spectroscopy. Many electronic phenomena often studied on small systems can be now forseen in macromolecular surroundings. This work considers the treatment with QM/MM tools of three electronic phenomena in biosystem: absoprtion, electronic attachment and core ionization. Latest developments of the Local Self-Consistent Field formalism (LSCF) have been used to treat delicate covalent junctions between the QM part and the MM part and the coupling of QM/MM and PCM methods. Firstly we have focussed on absorption spectra of chromophores embedded in macromolecules. The combined LSCF/MM and PCM approach have been employed to account for the electronic polarization when the chromophore absorbs one photon. This new method, called LSCF/MM\string:ERS has been tested and validated with the study of the absorption spectra on the squarain-tetralactam complex. Then, we have considered a fluorescent protein and decomposed the maximum absorption wavelength into several physical contributions. We have also analyzed the substitution effect of the chromophore. Secondly, the electronic capture have been studied on a cyclotide containing three disulfide bonds, which forms caracteristic hemi-bond (2c-3e) after irradiation. The last electronic phenomena studied is the core ionization tackled within the framework of the asymptotic projection approach. The latter has been implemented, then tested and validated on a set of molecules. This method have been employed to analyze the specific core ionization of glycine-containing systemes of increasing complexity, up to the Human Serum Albumin

Les flavonoïdes, molécules naturelles possédant des propriétés antiradicalaires et antioxydantes, sont produits au cours de cascades enzymatiques impliquant plusieurs enzymes. Il a récemment été proposé que certaines de ces enzymes s'assembleraient pour former un complexe multienzymatique transitoire, appelé métabolon, ancré à la membrane cellulaire. Cette structure rendrait possible des phénomènes de transfert direct de métabolites d'un site actif à l'autre (substrate channeling), réduisant ainsi les temps de diffusion et minimisant les effets de solvatation/désolvatation du substrat. L'objectif de ce travail est de proposer un premier modèle de ce type de complexe, impliquant trois enzymes de la biosynthèse des flavonoïdes : la dihydroflavonol-4-réductase (DFR), la flavonoïd-3'-hydroxylase (F3’H) et la leucoanthocyanidine réductase (LAR). L'étude de ces complexes moléculaires requiert la mise en œuvre d'une méthodologie multi-échelles basée sur l’utilisation i) de méthodes hybrides QM/MM pour l'étude de la réactivité enzymatique, ii) de simulations de dynamique moléculaire à résolution atomique se déroulant sur des échelles de temps de l'ordre de la microseconde pour estimer des propriétés thermodynamiques et cinétiques, iii) de calculs de docking protéine-protéine en résolution gros grain. L'application des différents niveaux de théorie nous a permis d'établir un premier modèle de métabolon à trois enzymes en interaction avec une membrane cellulaire. / Flavonoids, some natural compounds exhibiting antioxidant properties, are synthesized along enzymatic cascades involving several enzymes. It has been recently proposed that some of these enzymes are involved in the formation of large transient macromolecular edifices, called metabolon, interacting with cellular membrane. Such molecular complexes should allow direct metabolites transfer from one active site to the other (substrate channeling phenomenon), minimizing diffusion time and solvation effects. The present work aims to establish a first model of a metabolon involving 3 enzymes of the flavonoid biosynthesis: the dihydroflavonol 4-reductase (DFR), the flavonoid 3'-hydroxylase (F3'H) and the leucoanthocyanidin reductase (LAR). The study of such large molecular system requires a multiscale approach based on i) hybrid QM/MM methods to decipher enzymatic mechanism, ii) molecular dynamic simulations in microsecond timescale to estimate thermodynamic and kinetic properties and iii) protein-protein docking at coarse-grained resolution. These different levels of theory allow us to establish a first model of a three-enzymes-metabolon in interaction with a model of cellular membrane.