This dissertation consists of three major studies. The first study, described in Chapter 3, focuses on the experimental work we carried out; experimental study of the electronic transition dipole moment matrix elements (TDMM) for the and electronic transitions of the sodium dimer molecule. Here we obtained the electronic transition dipole moments through Autler-Townes and resolved fluorescence spectroscopy and compared them to the theory. The second study, described in Chapter 4, is on sodium dimer ion-pair states. In this work, we calculated the radiative lifetimes and electronic transition dipole moments between Na2 ion-pair states ( , , , ) and state. This study was published in 2015. The last study, described in Chapter 5, is the total lifetime (bound-bound plus bound-free) and transition dipole moment calculations of the ion-pair electronic states, , of the lithium dimer molecule. / Physics

Probing orientations of fluorescent molecules embedded in or attached to cell membranes has a great potential to reveal information on membrane structure and processes occurring in living cells. In this thesis, we first describe one- and two-photon linear dichroism measurements on a fluorescent probe embedded in a phospholipid membrane with a well- defined lipid composition. On the basis of experimental data, we determine the distribution of the angle between the one-photon transition dipole moment of the probe and the membrane normal. At the same time, we perform molecular dynamics simulations of the fluorescent probe and quantum calculations of its one-photon and two-photon absorption properties. By comparing the orientational distribution gained from experiments with that predicted by simulations, we test the ability of linear dichroism measurements to report on the orientation of a fluorescent molecule in a lipid membrane. We also examine the applicability of molecular simulations as a basis for the interpretation of experimental data.

The work presented in this thesis has striven toward improving the capability to study proteins using infrared (IR) spectroscopy. This includes development of new and improved experimental and theoretical methods to selectively observe and simulate protein vibrations. A new experimental method of utilising adenylate kinase and apyrase as helper enzymes to alter the nucleotide composition and to perform isotope exchange in IR samples was developed. This method enhances the capability of IR spectroscopy by enabling increased duration of measurement time, making experiments more repeatable and allowing investigation of partial reactions and selected frequencies otherwise difficult to observe. The helper enzyme mediated isotope exchange allowed selective observation of the vibrations of the catalytically important phosphate group in a nucleotide dependent protein such as the sarcoplasmic reticulum Ca2+-ATPase. This important and representative member of P-type ATPases was further investigated in a different study, where a pathway for the protons countertransported in the Ca2+-ATPase reaction cycle was proposed based on theoretical considerations. The transport mechanism was suggested to involve separate pathways for the ions and the protons. Simulation of the IR amide I band of proteins enables and supports structure-spectra correlations. The characteristic stacking of beta-sheets observed in amyloid structures was shown to induce a band shift in IR spectra based on simulations of the amide I band. The challenge of simulating protein spectra in aqueous medium was also addressed in a novel approach where optimisation of simulated spectra of a large set of protein structures to their corresponding experimental spectra was performed. Thereby, parameters describing the most important effects on the amide I band for proteins could be determined. The protein spectra predicted using the optimised parameters were found to be well in agreement with experiment. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.</p>

Fluorescent proteins (FPs) are the workhorses of biological molecular imaging. Important imaging modalities (such as polarization microscopy or FRET imaging) exploit anisotropic optical properties of fluorescent proteins. In this thesis, we present the results of our polarization microscopy and X-ray diffraction experiments on FP crystals, as well as mathematical interpretation of these results, yielding information on the directionality of one- and two-photon absorption within the investigated fluorescent protein molecules. For the anisotropy of one-photon absorption, we determine the transition dipole moment (TDM) orientations in three representative fluorescent proteins. Validation with available quantum mechanical predictions values and an experimentally determined TDM orientation of the GFP gives confidence to the results obtained. For the two-photon absorption, we first test our hypothesis that two-photon absorptivity tensors of representative FPs exhibit vector-like behaviour and then examine the applicability of this simplification as a basis for the interpretation of our two-photon polarization microscopy data.

No description available.

Nous investiguons dans ce travail la dynamique des excitons dans une couche mince d’agrégats H autoassemblés hélicoïdaux de molécules de sexithiophène. Le couplage intermoléculaire (J=100 meV) place ce matériau dans la catégorie des semi-conducteurs à couplage de type intermédiaire. Le désordre énergétique et la forte interaction électronsphonons causent une forte localisation des excitons. Les espèces initiales se ramifient en deux états distincts : un état d’excitons autopiégés (rendement de 95 %) et un état à transfert de charge (rendement de 5%). À température de la pièce (293K), les processus de sauts intermoléculaires sont activés et l’anisotropie de la fluorescence décroît rapidement à zéro en 5 ns. À basse température (14K), les processus de sauts sont gelés. Pour caractériser la dynamique de diffusion des espèces, une expérience d’anisotropie de fluorescence a été effectuée. Celle-ci consiste à mesurer la différence entre la photoluminescence polarisée parallèlement au laser excitateur et celle polarisée perpendiculairement, en fonction du temps. Cette mesure nous donne de l’information sur la dépolarisation des excitons, qui est directement reliée à leur diffusion dans la structure supramoléculaire. On mesure une anisotropie de 0,1 après 20 ns qui perdure jusqu’à 50ns. Les états à transfert de charge causent une remontée de l’anisotropie vers une valeur de 0,15 sur une plage temporelle allant de 50 ns jusqu’à 210 ns (période entre les impulsions laser). Ces résultats démontrent que la localisation des porteurs est très grande à 14K, et qu’elle est supérieure pour les espèces à transfert de charge. Un modèle numérique simple d’équations différentielles à temps de vie radiatif et de dépolarisation constants permet de reproduire les données expérimentales. Ce modèle a toutefois ses limitations, notamment en ce qui a trait aux mécanismes de dépolarisation des excitons. / In this work, we investigate exciton dynamics in a thin film of sexithiophene molecules in self-assembled chiral H-aggregate supramolecular stacks. The intermolecular coupling energy J=100 meV places those molecules in the intermediate coupling regime. The energetic disorder and the strong phonon-electron interactions leads to high localization of the photoexcitations. The initial photoexcited species branches into two distinct states : self-trapped exciton (95% yield) and charge-transfer excitons (5% yield). At room temperature (293K), the intermolecular hopping processes are thermaly activated and the fluorescence anisotropy goes to zero within 5 ns. At low temperature (14K), hopping processes are frozen. To characterize exciton diffusion mechanisms, a fluorescence anisotropy experiment has been done. This measurement consists of monitoring the difference between the parallel and perpendicular composants of the photoluminescence (with respect to the laser beam), as a function of time. The fluorescence anisotropy gives us information about the depolarization of the excitons, which is directly connected with their diffusion within the supramolecular stack. We measure an anisotropy of 0,1 after 20 ns which stays constant for 50 ns. Chargetransfer states induce a rise of the anisotropy up to 0,15 between 50 ns and 210 ns (the period between adjacent laser pulses). Those measurements shows that exciton localization is very strong at 14K and higher for the charge-transfer states than the self-trapped ones. A simple mathematical model based on the resolution of a system of differential equations with constants radiative and depolarization lifetimes can reproduce the experimental data. This model has some limitations, especially for the description of the depolarization mechanisms of the self-trapped excitons.

Nous investiguons dans ce travail la dynamique des excitons dans une couche mince d’agrégats H autoassemblés hélicoïdaux de molécules de sexithiophène. Le couplage intermoléculaire (J=100 meV) place ce matériau dans la catégorie des semi-conducteurs à couplage de type intermédiaire. Le désordre énergétique et la forte interaction électronsphonons causent une forte localisation des excitons. Les espèces initiales se ramifient en deux états distincts : un état d’excitons autopiégés (rendement de 95 %) et un état à transfert de charge (rendement de 5%). À température de la pièce (293K), les processus de sauts intermoléculaires sont activés et l’anisotropie de la fluorescence décroît rapidement à zéro en 5 ns. À basse température (14K), les processus de sauts sont gelés. Pour caractériser la dynamique de diffusion des espèces, une expérience d’anisotropie de fluorescence a été effectuée. Celle-ci consiste à mesurer la différence entre la photoluminescence polarisée parallèlement au laser excitateur et celle polarisée perpendiculairement, en fonction du temps. Cette mesure nous donne de l’information sur la dépolarisation des excitons, qui est directement reliée à leur diffusion dans la structure supramoléculaire. On mesure une anisotropie de 0,1 après 20 ns qui perdure jusqu’à 50ns. Les états à transfert de charge causent une remontée de l’anisotropie vers une valeur de 0,15 sur une plage temporelle allant de 50 ns jusqu’à 210 ns (période entre les impulsions laser). Ces résultats démontrent que la localisation des porteurs est très grande à 14K, et qu’elle est supérieure pour les espèces à transfert de charge. Un modèle numérique simple d’équations différentielles à temps de vie radiatif et de dépolarisation constants permet de reproduire les données expérimentales. Ce modèle a toutefois ses limitations, notamment en ce qui a trait aux mécanismes de dépolarisation des excitons. / In this work, we investigate exciton dynamics in a thin film of sexithiophene molecules in self-assembled chiral H-aggregate supramolecular stacks. The intermolecular coupling energy J=100 meV places those molecules in the intermediate coupling regime. The energetic disorder and the strong phonon-electron interactions leads to high localization of the photoexcitations. The initial photoexcited species branches into two distinct states : self-trapped exciton (95% yield) and charge-transfer excitons (5% yield). At room temperature (293K), the intermolecular hopping processes are thermaly activated and the fluorescence anisotropy goes to zero within 5 ns. At low temperature (14K), hopping processes are frozen. To characterize exciton diffusion mechanisms, a fluorescence anisotropy experiment has been done. This measurement consists of monitoring the difference between the parallel and perpendicular composants of the photoluminescence (with respect to the laser beam), as a function of time. The fluorescence anisotropy gives us information about the depolarization of the excitons, which is directly connected with their diffusion within the supramolecular stack. We measure an anisotropy of 0,1 after 20 ns which stays constant for 50 ns. Chargetransfer states induce a rise of the anisotropy up to 0,15 between 50 ns and 210 ns (the period between adjacent laser pulses). Those measurements shows that exciton localization is very strong at 14K and higher for the charge-transfer states than the self-trapped ones. A simple mathematical model based on the resolution of a system of differential equations with constants radiative and depolarization lifetimes can reproduce the experimental data. This model has some limitations, especially for the description of the depolarization mechanisms of the self-trapped excitons.

Fundação de Amparo a Pesquisa do Estado de Minas Gerais / In this work we made a theoretical study of absorption line-shape of poly (pphenylene vinylene) (PPV). The model was applied in films processed by techniques: spin-coating (SC), layer-by-layer (LbL), and Langmuir-Blodgett (LB). The probability of electronic transitions was calculated based on the molecular model of excitons, Franck-Condon states, Gaussian distribution of non-entangled chains with conjugate degree n, semi-empirical parameterization of energy gap, electric dipole moment, and electron-vibrational mode coupling. Based on the approach of the energy gap functional dependence 1/n, the inclusion of the non-homogeneity energy dispersion 1/n2 is essential to obtain good experimental data agreement, mainly, where the absorption spectra display peaks width of about 65 meV. For unresolved absorption spectra, such as those observed for a large number of conjugated polymers processed via spin-coating technique, for example, the non-homogeneity energy dispersion parameterization is not significant. We develop a model to describe the possible chemical reactions of conversion of poly(xylyliden tetrahydrothiophenium chloride) (PTHT) monomers to PPV monomers and PPV monomers in others monomers of different degrees of conjugation. The dependence 1/n of the functional energy gap was compared with experimental data oligomers and calculations optimized geometry by Density Functional Theory (DFT). Effects of exciton confinement were considered in the transition dipole moment functional. Simulations to calculate the oscillator strength of the absorption spectra in PPV oligomers indicate that the HOMO-LUMO state prevails over other excited states. Results obtained from the use of the distribution of the random walk are as good as those achieved by the use of Gaussian distribution of conjugated segments in simulations of absorption spectra of the PPV. The use of transition dipole moment functional, which includes the effect of exciton confinement together with the distribution of the random walk provide good results in adjustments theoretical absorption spectra of PPV with more consistent physical parameters. / Nesse trabalho fizemos um estudo teórico da forma de linha de absorção do poli(p-fenileno vinileno) (PPV). O modelo foi aplicado em filmes processados pelas técnicas: spin-coating (SC), layer-by-layer (LbL) e Langmuir-Blodgett (LB). A probabilidade de transição eletrônica foi calculada com base no modelo do exciton molecular, estados de Franck-Condon, distribuição Gaussiana de cadeias não emaranhadas com grau de conjugação n, parametrização semi-empírica do gap de energia, do momento de dipolo elétrico e do acoplamento eletrônico vibracional. Baseamos na aproximação do funcional do gap de energia de dependência 1/n, a inclusão da dispersão de energia não homogênea 1/n2, que é essencial para se obter uma boa concordância com os dados experimentais, principalmente em casos, onde o espectro de absorção apresenta picos com largura de aproximadamente 65 meV. Em espectros de filmes pouco definidos, tais como os processados pela técnica spin-coating, a dispersão de energia não homogênea não é significativa. Desenvolvemos um modelo para descrever as possíveis reações químicas de conversão de monômeros de poli- (cloreto de xilideno tetrahidrotiofeno) (PTHT) em PPV e de monômeros de PPV em outros de diferentes graus de conjugação. A dependência 1/n do funcional do gap de energia foi comparada com dados experimentais de oligômeros de PPV e cálculos otimizados da geometria pela Teoria do Funcional da Densidade (DFT). Efeitos de confinamento de exciton foram considerados no funcional do momento de dipolo de transição eletrônica. Simulações feitas para calcular a força de oscilador no espectro de absorção em oligômeros de PPV indicam que o estado HOMO-LUMO prevalece sobre outros estados excitados. Resultados obtidos pelo uso da distribuição do passeio aleatório são tão bons quanto aos realizados pelo uso da distribuição Gaussiana de segmentos conjugados em simulações de espectros de absorção do PPV. O uso do funcional do momento de dipolo de transição, que inclui efeito de confinamento de excitons, junto com a distribuição do passeio aleatório propiciam bons resultados nos ajustes teóricos de espectros de absorção do PPV com parâmetros físicos mais consistentes. / Doutor em Física