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Luminescence properties of flexible conjugated dyesSjöqvist, Jonas January 2012 (has links)
In this licentiate thesis the luminescence properties of two flexible conjugated dyes have been studied. The first, Pt1, is a platinum(II) acetylide chromophore used in optical power limiting materials. The second is a set of optical probes known as luminescent conjugated oligothiophenes (LCOs), which are used to detect and characterize the protein structures associated with amyloid diseases such as Alzheimer’s disease. MM3 and CHARMM force field parameters have been derived for the Pt1 chromophore and LCOs, respectively, based on potential energy surface references calculated at the density functional theory (DFT)/B3LYP level of theory. The parameters have been used to perform room temperature molecular dynamics simulations of the chromophores in solvent, where tetrahydrofuran was used for Pt1 and water for the LCOs. Conformationally averaged absorption spectra were obtained, based on response theory calculations at the time-dependent DFT(TDDFT)/CAM-B3LYP level of theory for a selection of structures from the simulations. For one of the LCOs, p-HTAA, force field parameters were also created describing the dominant first excited state, based on TDDFT/B3LYP reference potential energy surfaces. These were used for molecular dynamics simulations of the chromophore in the excited state, allowing the creation of an emission spectrum. A theoretically obtained Stokes shift of 112 nm could be computed based on the absorption and emission spectra, which is in good agreement with the experimental value of 124 nm. In addition, a quantum mechanics/molecular mechanics study of the effects of solvation on the absorption properties of the p-HTAA chromophore in water has been conducted, resulting in two models for including these effects in the averaged spectra. The first includes explicit water molecules in the form of point charges and polarizable dipole moments, and results in an absorption wavelength that is blueshifted by 2 nm from a high quality reference calculation. The second model involves the complete removal of the solvent as well as the ionic groups of the chromophore. The resulting absorption wavelength is blueshifted by an additional 4 nm as compared to the first model, but requires only one fifth of the computational resources.
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Understanding the Relationship Between Thermal and Photochemical Isomerization in Visual ReceptorsGozem, Samer 24 July 2013 (has links)
No description available.
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Développement d’un schéma de couplage QM/MM (Quantum Mechanic / Molecular Mechanic) pour les états excités localisés dans les matériaux hybrides organique-inorganiques / Development of a QM /MM (Quantum Mechanic / Molecular Mecanic) coupling scheme for the excited states localized in the organic-inorganic hybrid materialsFayon, Pierre 16 December 2011 (has links)
Ces dernières années, la mise au point de matériaux hybrides organique-inorganiques a fait l’objet d’un intérêt grandissant dans le domaine de la chimie verte. Les matériaux hybrides a base de silice fonctionnalisée par des molécules organiques possèdent des propriétés modulables, permettant leur application dans plusieurs domaines (photochimie, médecine, dépollution . . .). D’un point de vue théorique, le challenge d’une telle étude résulte dans la détermination des propriétés d’optiques. En effet, la taille de ces systèmes ne permet pas un traitement de ces derniers d’un point de vue strictement quantique. L’enjeu de ce travail de recherche est le développement d’un programme qm/mm/tddft (Quantum Mechanic/Molecular Mechanic/ Time Dependant Density Functional Theory), pour le calcul des états électroniques excités localisés dans les solides, avec une applicationparticulière au domaine UV-visible dans les matériaux hybrides organique-inorganiques.Dans la pratique, l’intégration des équations classiques du mouvement de tous les noyaux est effectuée par le programme de dynamique moléculaire dl poly, tandis que les contributions aux forces issues des atomes dans la partie de la simulation quantique sont évaluées par le code siesta en utilisant la méthode dft (Density Functional Theory). Les spectres électroniques seront calculés avec un nouveau code de tddft (Time Dependant Density Fuctional Theory) développé pour ce projet, dans lequel l’utilisation d’une base de produits dominants accélère le calcul de façon notable. / Last years, the development of organic-inorganic hybrid materials has been a growing interest in the field of green chemistry. Hybrid materials based on silica functionalized with organic molecules have flexible properties, allowing their application in several fields (photochemistry, medicine, ...). From a theoretical point of view, the challenge of such a study results in determination of the optical properties. Indeed, the size of the system does not allow treatment with a purely quantum theory. The aim of this research is to develop a qm/mm/tddft (Quantum Mechanic / Molecular Mechanic / Time Dependent Density Functional Theory) code to calculate the excited electronic states localized in solids, with a particular application for the UV-visible region in organic-inorganic hybrid materials. In practice, the integration of classical equations of motion of all the nuclei are made by the molecular dynamics program dl poly, while contributions from the forces in the quantum simulation are evaluated by using the code siesta with the dft (Density Functional Theory) method . The electronic spectra are calculated with a new tddft code developed for this project, in which the use of dominants products accelerates the calculation significantly.
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Biomimetic and Theoretic Investigations of Unusual Iron-Sulphur Clusters / Biomimetische und Theoretische Untersuchungen ungewöhnlicher Eisen-Schwefel-ClusterFuchs, Michael Günther Georg 21 October 2009 (has links)
No description available.
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Estudos de mecanismos redox enzimáticos por eletroquímica e modelagem computacional / Studies of enzymatic redox mechanisms by electrochemistry and computational modelingCallera, Welder Franzini Amaral [UNESP] 04 August 2017 (has links)
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Previous issue date: 2017-08-04 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Esta tese de doutoramento apresentou o entendimento de processos redox enzimáticos, detalhando o mecanismo envolvido na troca eletrônica, a qual resulta na formação de um produto, por catálise enzimática. Observou-se a influência de um eletrodo sob a ação de um potencial estacionário aplicado (E) na reação enzima/substrato. Realizou-se eletroanálises, como: Voltametria Cíclica (VC) e Espectroscopia de Impedância Eletroquímica (EIE), para a penicilinase. Os resultados obtidos dão indícios de que a reação enzimática se beneficia de determinados potenciais, pois o parâmetro utilizado, Rct, resistência à transferência de cargas, sugere que ocorre maior troca eletrônica em alguns potenciais ótimos (faixa de -0,3 a -0,5 V). A Simulação Molecular serviu para estudar o comportamento atomístico por métodos clássicos (Dinâmica Molecular – DM) para as condições impostas experimentalmente, esclarecendo o mecanismo de reação enzimática por métodos quânticos (DFT – Teoria do Funcional de Densidade) e híbridos (QM/MM), cabendo salientar que a penicilinase não pertence à classe das enzimas oxirredutivas. / This doctoral thesis presented the understanding of enzymatic redox processes, detailing the mechanism involved in the electronic exchange, which results in the formation of a product by enzymatic catalysis. The influence of an electrode under the action of an applied stationary potential (E) on the enzyme/substrate reaction was observed. Electroanalysis was performed, such as: Cyclic Voltammetry (VC) and Electrochemical Impedance Spectroscopy (EIS), for the penicilinase. The results obtained indicate that the enzymatic reaction benefits from certain potentials, since the parameter used, Rct, resistance to the transfer of charges, suggests that there is greater electronic exchange in some optimal potentials (range the -0.3 to -0.5 V). The Molecular Simulation was used to study the atomistic behavior by classical methods (Molecular Dynamics - DM) for experimentally imposed conditions, clarifying the mechanism of enzymatic reaction by quantum methods (DFT) and hybrids (QM/MM). That penicillinase does not belong to the class of oxidoreductive enzymes.
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Etudes théoriques des propriétés optiques linéaires et non-linéaires des biomolécules. / Theoretical studies of linear and non-linear optical properties of biomoleculesBonvicini, Andrea 24 October 2019 (has links)
Dans cette thèse, les propriétés optiques de biomolécules importantes ont été étudiées en utilisant une approche théorique et, dans un cas, aussi expérimentale. La Théorie de la fonctionnelle de la densité (DFT) et la timedependent-DFT (TD-DFT) sont les principales méthodes de chimie quantique utilisées dans cette thèse. Plusieurs spectroscopies ont été étudiées (au niveau théorique et, dans certains cas, également au niveau expérimental) : absorption électronique linéaire (absorption à un photon, OPA) et non-linéaire (absorption à deux ou trois photons, TPA et 3PA), dichroïsme circulaire électronique (DCE) et spectroscopie de fluorescence. Les effets de l’environnement, particulièrement importants dans des systèmes biologiques, ont été pris en compte, pour les propriétés de l’état fondamental et des états excités en utilisant une méthode multi-échelles QM/MM appelée Polarizable Embedding (PE). L’échantillonnage des conformations a été pris en compte avec des simulations de dynamique moléculaire (MD) qui sont basées sur la mécanique classique. Deux thématiques ont été étudiées dans cette thèse : le cholestérol et le design in silico de ses analogues fluorescents ainsi que la caractérisation des coudes de type β dans différentes conformations grâce à la simulation des spectres DCE. La simulation de plus d’une spectroscopie a été importante dans l’étude des états excités du cholestérol dans des solutions organiques. Le design in silico a suggéré un nouveau stérol-polyénique (P-stérol) qui montre despropriétés optiques améliorées pour le mécanisme d’excitation à trois photons par rapport au déhydroergostérol (DHE), une sonde du cholestérol déjà très utilisée. Ce nouveau P-stérol a été suggéré pour la synthèse. L’étude des spectres de DCE des coudes β en différentes conformations a mené une double conclusion : même si deux allures de DCE pour les conformations des coudes β étudiées (4) ont été trouvées (dans la majorité des cas), la spectroscopie de DCE doit toujours être associée à d’autres techniques spectroscopiques dans la caractérisation en solution des coudes β. / In this thesis, the optical properties of important biomolecules were studied using a theoretical approach and, in one case, also an experimental one. Density Functional Theory (DFT) and time-dependent-DFT (TD-DFT), were the principal quantum chemical methods adopted in this thesis.Various spectroscopies were studied (theoretically and, in some cases, also experimentally) : linear (one-photon, OPA) and non-linear (two- and three-photon, TPA and 3PA) electronic absorption, electronic circular dichroism (ECD) and fluorescence spectroscopy. The environment effects, which are particularly important in biological systems, were taken into account, for both ground and excited states properties, using a multiscale QM/MM method called Polarizable Embedding (PE). The sampling of conformations was addressed by Molecular Dynamic (MD) simulations based on classical mechanics. Two topics were studied in this thesis: cholesterol and the in-silico design of its fluorescent analogues, and the characterization of β-turns in different conformations by simulations of their ECD spectra in aqueous solutions. The simulation of more than one spectroscopy resulted to be important when studying the electronic excited states of cholesterol in organic solutions. The in-silico design study suggested a novel polyene-sterol (P-sterol) which shows improved optical properties for the three-photon excitation mechanism with respect to dehydroergosterol (DHE), an already widely used cholesterol probe. This new P-sterol was thus suggested for synthesis. The achievement from the study of ECD spectra for different β-turn conformations is two-fold: even if two ECD patterns for the β-turn conformations studied (4) were found (in most of cases), ECD spectroscopy should be always associated with other spectroscopic techniques when trying to characterize the β-turn conformations in solutions.
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Energetic and Microscopic Characterization of the Primary Electron Transfer Reaction in the (6-4) Photolyase Repair ReactionOßwald, Mara 17 April 2024 (has links)
Wird DNA mit UV-Licht bestrahlt, kommt es zur Bildung von Photoschäden, die zu Zelltod oder Krebs führen können. In dieser Arbeit wird die primäre Elektronentransferreaktion des lichtaktivierten Reparaturprozesses des (6-4)-Schadens in Drosophila melanogaster charakterisiert. Der katalytische Reparaturzyklus wird durch das Flavoprotein (6-4)-Photolyase (PL) realisiert. Der Elektronentransfer (ET) vom Flavin-Adenin-Dinukleotid (FADH⁻) Kofaktor zum Schaden initiiert die molekularen Umlagerungen. Diese Arbeit charakterisiert die primäre ET Reaktion mithilfe von molekulardynamischen Langzeitsimulationen (µs) in Kombination mit Quantenmechanik/Molekularmechanik-Simulationen. Ab initio lokale Coupled-Cluster- und Dichtefunktionaltheorierechnungen wurden angewendet, um die relative Energetik von lokal angeregten und Ladungstransferzuständen des (6-4)-Reparaturkomplexes zu charakterisieren. Es zeigt sich, dass die Reduktion des (6-4)-Schadens durch einen Ladungstransferzustand ermöglicht wird an dem die Adeninstruktur des FADH⁻ -Kofaktors beteiligt ist. Über die Simulationen wird ein mikroskopisches Bild der Reaktionskoordinate der Elektronentransferreaktion im Marcusbild entwickelt. Diese ist nicht vollständig durch parabolische freie Energiekurven beschrieben sondern wird, durch Wechselwirkungen in der aktiven Tasche, ein Multiminima-Reaktionspfad ausgebildet. Hierbei hat die Rotation der Seitenkette der benachbarten, geladenen Aminosäure Lys246 dominanten Einfluss. Dies legt nahe, dass die primäre ET Reaktion der (6-4) Schadensreparatur, einen vom Adenin unterstützten ET Weg von der PL zur 5’ Seite des Schadens nimmt. Dieser Prozess wird durch benachbarte Aminosäuren und einer Stärkung der Wasserstoffbrücken mit Wassermolekülen stabilisiert. Die Ergebnisse dieser Arbeit zeigen, dass ET-Reaktionen in komplexen enzymatischen Systemen nicht im Kontinuumsbild von ET beschrieben werden können, da lokale Wechselwirkungen drastischen Einfluss auf die ET Reaktionen haben. / UV-light irradiation of DNA leads to the formation of photolesions that can cause cell death and cancer. This thesis aims at the characterization of the primary electron transfer (ET) reaction in the photoactivated repair process of the (6-4) lesion in Drosophila melanogaster. The catalytic repair cycle is realized by a flavoprotein called photolyase (PL). The ET from the fully reduced flavin-adenine-dinucleotide (FADH⁻) cofactor of the PL to the lesion initiates molecular rearrangements. In this thesis fluctuation properties of the enzyme environment on the excited states are considered by conducting long-time (µs) molecular dynamics simulations combined with extensive quantum mechanical/molecular mechanical simulations. Ab initio local coupled cluster simulations and density functional theory are applied to characterize the relative energetics of locally excited and charge transfer (CT) states in the (6-4) lesion repair complex. Reduction of the (6-4) lesion is found to be enabled by a CT state involving the adenine moiety of the FADH⁻ cofactor. Microscopic characterization of a Marcus-type free energy reaction coordinate reveals that it cannot be fully described by parabolic free energy curves. Specifically, rotation of the side chain of nearby charged amino acid Lys246 imposes a double-well character on the potential energy surface along the reaction coordinate of the ET. For the ET reaction triggering the catalytic (6-4) lesion repair, the findings of this thesis suggest an ET pathway to the 5’ side of the (6-4) lesion mediated by the adenine moiety. The process is stabilized by neighboring amino acids and a strengthening of hydrogen bonds with water molecules. The presented results demonstrate that ET reactions in complex enzymatic systems cannot be described within the continuum ET picture, as local interactions drastically tune the ET reaction.
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Theoretical Description of Electronic Transitions in Large Molecular Systems in the Optical and X-Ray RegionsList, Nanna Holmgaard January 2015 (has links)
The size and conformational complexity of proteins and other large systems represent major challenges for today's methods of quantum chemistry.This thesis is centered around the development of new computational tools to gain molecular-level insight into electronic transitions in such systems. To meet this challenge, we focus on the polarizable embedding (PE) model, which takes advantage of the fact that many electronic transitions are localized to a smaller part of the entire system.This motivates a partitioning of the large system into two regions that are treated at different levels of theory:The smaller part directly involved in the electronic process is described using accurate quantum-chemical methods, while the effects of the rest of the system, the environment, are incorporated into the Hamiltonian of the quantum region in an effective manner. This thesis presents extensions of the PE model with theaim of expanding its range of applicability to describe electronic transitions in large molecular systemsin the optical and X-ray regions. The developments cover both improvements with regardto the quantum region as well as the embedding potential representing the environment.Regarding the former, a damped linear response formulation has been implemented to allow for calculations of absorption spectra of large molecular systems acrossthe entire frequency range. A special feature of this development is its abilityto address core excitations that are otherwise not easily accessible.Another important development presented in this thesis is the coupling of the PE model to a multi-configuration self-consistent-field description of the quantum region and its further combination with response theory. In essence, this extends the PE model to the study of electronic transitions in large systems that are prone to static correlation --- a situation that is frequently encountered in biological systems. In addition to the direct environmental effects on the electronic structure of the quantum region, another important component of the description of electronic transitions in large molecular systems is an accurate account of the indirect effects of the environment, i.e., the geometrical distortions in the quantum region imposed by the environment. In thisthesis we have taken the first step toward the inclusion of geometry distortions in the PE frameworkby formulating and implementing molecular gradients for the quantum region. To identify critical points related to the environment description, we perform a theoretical analysis of the PE model starting from a full quantum-mechanicaltreatment of a composite system. Based on this, we present strategies for an accurate yet efficient construction of the embedding potentialcovering both the calculation of ground state and transition properties. The accurate representation of the environment makes it possible to reduce the size of the quantum region without compromising the overall accuracy of the final results. This further enables use of highly accurate quantum-chemical methods despite their unfavorable scaling with the size of the system. Finally, some examples of applications will be presented to demonstrate how the PE model may be applied as a tool to gain insight into and rationalize the factors influencing electronic transitions in large molecular systems of increasing complexity. / <p>The dissertation was awarded the best PhD thesis prize 2016 by the Danish Academy of Natural Sciences.</p><p></p><p>QC 20170209</p>
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Solar Energy Conversion in Plants and Bacteria Studied Using FTIR Difference Spectroscopy and Quantum Chemical Computational MethodologiesParameswaran, Sreeja 15 July 2009 (has links)
This dissertation presents a study of the molecular mechanism underlying the highly efficient solar energy conversion processes that occur in the Photosystem I (PS I) reaction centers in plants and bacteria. The primary electron donor P700 is at the heart of solar energy conversion process in PS I and the aim is to obtain a better understanding of the electronic and structural organization of P700 in the ground and excited states. Static Fourier Transform Infra-Red (FTIR) difference spectroscopy (DS) in combination with site directed mutagenesis and Density Functional Theory (DFT) based vibrational frequency simulations were used to investigate how protein interactions such as histidine ligation and hydrogen bonding modulate this organization. (P700+-P700) FTIR DS at 77K were obtained from a series of mutants from the cyanobacterium Synechocystis sp. 6803 (S. 6803) where the amino acid residues near the C=O groups of the two chlorophylls of P700 where specifically changed. (P700+-P700) FTIR DS was also obtained for a set of mutants from C. reinhardtii where the axial ligand to A0-, the primary electron acceptor in PS I was modified. The FTIR DS obtained from these mutants provides information on the axial ligands, the hydrogen bonding status as well as the polarity of the environment of specific functional groups that are part of the chlorophyll molecules that constitute P700. Assignment of the FTIR bands to vibrational modes in specific types of environment is very difficult. In order to assist the assignment of the difference bands in experimental spectra DFT based vibrational mode frequency calculations were undertaken for Chl-a and Chl-a+ model molecular systems under different set of conditions; in the gas phase, in solvents using the Polarizable Continuum Model (PCM), in the presence of explicit solvent molecules using QM/MM methods, and in the presence of axial ligands and hydrogen bonds. DFT methods were also used to calculate the charge, spin and redox properties of Chl-a/Chl-a’ dimer models that are representative of P700, the primary electron donor in PS I.
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Étude du comportement dynamique de systèmes catalytiques greffés sur silice.Halbert, Stéphanie 04 July 2013 (has links) (PDF)
Ce mémoire présente une méthodologie théorique pour comprendre l'origine de différence de comportement dynamique de complexes alkylidènes, catalyseurs de type Schrock de la métathèse des oléfines, greffés un support de silice amorphe. Dans un travail antérieur, les différences entre les valeurs de l'anisotropie de déplacement chimique (CSA) obtenues par des mesures de RMN du solide et celles estimées par le calcul pour des systèmes figés avaient conduit à suggérer des régimes dynamiques différents pour ces complexes, certains étant proposés comme immobiles, d'autres comme mobiles. Dans le premier groupe se trouve les complexes du molybdène et dans le second les complexes du tungstène, rhénium et tantale. Dans le cadre de cette thèse, nous nous sommes donc attachés à mettre en place une méthodologie pour déterminer ces CSA et donc la nature de la dynamique de chaque système qui conduit au CSA moyenné. Nous nous sommes d'abord intéressés à des systèmes moléculaires pour révéler des interactions non covalentes entre les complexes et le support silice à partir d'une approche de type petit cluster en utilisant divers niveaux de calculs DFT et modèles moléculaires. Cette modélisation moléculaire de la silice étant insuffisante, nous avons entrepris une modélisation de la surface de silice amorphe par dynamique moléculaire classique dont les caractéristiques ont été comparées aux données expérimentales existantes. Le comportement dynamique de ces systèmes greffés sur silice amorphe a été simulé par dynamique moléculaire ab initio QM/MM, couplant une description quantique du complexe organométallique à une description classique du support. Ces études dynamiques ont conduit à des valeurs de CSA moyennées dans le temps de la dynamique. La comparaison de ces valeurs calculées et des valeurs expérimentales a permis d'apporter des éléments de réponse sur l'origine des différences de comportement dynamique de ces complexes alkylidènes. De façon remarquable des mouvements d'ensemble des espèces greffées par rapport à la surface de silice et des modification de la coordination du métal par l'apparition d'interaction agostique contribuent à moyenner le CSA.
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