Les protéines fluorescentes sont très largement utilisées dans les études de biologie moléculaire depuis maintenant une vingtaine d’année. Pour autant, l’origine de leurs propriétés photophysiques n’est pas totalement élucidée. Dans cette thèse, nous avons essayé d’améliorer la compréhension de la photophysique de deux protéines fluorescentes particulières : Padron et EosFP.Dans la protéine Padron, nous avons étudié l’isomérisation du chromophore et cherché à déterminer si la protonation et l’isomérisation sont simultanées ou successives. Pendant l’isomérisation, le donneur de proton potentiel est le résidu Tyr159. Nous avons d’abord montré que dans le vide, le transfert de proton est peu probable quelle que soit la géométrie du chromophore. Dans la protéine (où l’effet de l’environnement n’est pas négligeable) nous avons mis en évidence par dynamique moléculaire que, durant l’isomérisation, le transfert de proton n’est presque jamais favorable et reste donc un marginal.Par ailleurs, ces mêmes dynamiques ont montré que, à la fin de l’isomérisation, il apparaît de nombreux chemins de molécules d’eau reliant le chromophore au solvant et pouvant permettre un transfert de proton. On conclut doncque l’isomérisation et la protonation ne sont pas simultanées mais successives.Dans le cas de la protéine EosFP, nous avons analysé l’effet d’une molécule d’eau présente dans une partie des structures cristallines. Les dynamiques avec le chromophore à l’état fondamental ont montré que cette molécule ne joue pas de rôle, que ce soit sur le réseau de liaison hydrogène ou sur le spectre d’absorption. Par contre, à l’état excité, les dynamiques ont montré que l’extinction de fluorescence est beaucoup plus rapide sans la molécule d’eau qu’en sa présence.Par ailleurs, ces dynamiques ont mis en évidence que la protéine bloque souvent le chromophore dans des géométries où il ne peut pas retourner à l’état fondamental ni par fluorescence, ni par conversion interne. Ces géométries « noires» jouent un rôle important dans la photophysique.Pour tenir compte de ces géométries, nous avons calculé le rendement quantique et le temps de vie de fluorescence par intégration directe le long des trajectoires et par cinétique chimique. Dans les deux cas, nous avons obtenu un accord qualitatif avec l’expérience. / Fluorescent proteins are widely used in biology studies since 20 years. Yet, the origin of their photophysical properties aren’t totally explained. Here, we try to improve the understanding of two particular fluorescent proteins: Padron and EosFP.In the protein Padron, we work on the isomerization of chromophore and try to determine whether isomerization and protonation are simultaneous or successive processes. During the isomerization, the potential donor is Tyr159.First, we show that, in vacuum, the proton transfer is quite unlikely whatever the chromophore geometry.In the protein (where the environment effect isn’t negligible) we evidence with molecular dynamics that, during isomerization, proton transfer stays marginal.In addition, these dynamics shown the appearance, at the end of isomerization, of a lot of water molecules channel between the chromophore and the solvent allowing a proton transfer. We conclude that isomerization and protonation are successive processes.In the case of the protein EosFP, we first analyze the effect of a water molecule which is found only in some of the crystallographic structures.Molecular dynamics of the protein with the chromophore in the ground state show that the water molecule doesn’t play any role neither in the hydrogen bond network nor in the absorption spectra.On the contrary, in the excited state, dynamics without this water show a significant faster decay of fluorescence that those with the molecule.In addition, those dynamics have demonstrate that during long period, the protein retains the chromophore in geometries in which it is unable to convert to the ground state, neither by fluorescence nor by internal conversion. Those “dark” geometries play a crucial role in the photophysics.To take them into account, we calculate the quantum yield and the fluorescence lifetime by direct integration along trajectories and by a kinetic scheme. We obtain a good qualitative agreement with the two methods.

The National Academy of Sciences recently published a report which calls for improvements to the field of forensic science. Their report criticized many forensic disciplines for failure to establish rigorously-tested methods of comparison, and encouraged more research in these areas to establish limitations and assess error rates. This study applies chemometric and statistical methods to current and developing analytical techniques in fiber analysis. In addition to analysis of commercially available dyed textile fibers, two pairs of dyes are selected based for custom fabric dyeing on the similarities of their absorbance spectra and dye molecular structures. Visible absorption spectra for all fiber samples are collected using microspectrophotometry (MSP) and mass spectra are collected using electrospray ionization (ESI) mass spectrometry. Statistical calculations are performed using commercial software packages and software written in-house. Levels of Type I and Type II error are examined for fiber discrimination based on hypothesis testing of visible absorbance spectra using a nonparametric permutation method. This work also explores evaluation of known and questioned fiber populations based on an assessment of p-value distributions from questioned-known fiber comparisons with those of known fiber self-comparisons. Results from the hypothesis testing are compared with principal components analysis (PCA) and discriminant analysis (DA) of visible absorption spectra, as well as PCA and DA of ESI mass spectra. The sensitivity of a statistical approach will also be discussed in terms of how instrumental parameters and sampling methods may influence error rates.

No description available.

<p>Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin. </p><p>The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work.</p><p>The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-<i>Z,syn</i> configuration (in the inactive form of the protein) to C15-<i>E,anti</i> (in the active form). In this work, a reaction mechanism for this isomerization is proposed. </p><p>DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied.</p><p>Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.</p>

Pour notre travail de thèse, nous avons établi une méthodologie, basée sur la DFT et sa variante dépendante du temps, qui permet l'évaluation efficace et la prédiction rapide des couleurs de différentes familles de colorants carbonylés dans différents environnements. Ainsi, nous sommes capables de fournir des valeurs théoriques très précises pour les énergies de transition des dérivés de l'anthraquinone, de la coumarine et de l'indigo ainsi que du thioindigo. Notre stratégie prend en compte aussi bien les effets de solvatation, dans le cadre d'une modélisation en continuum, que les effets du pH, sur la position de la bande d'absorption maximale du spectre UV/VIS. / The project of the Ph. D. work consists in the elaboration of a theoretical methodology able to evaluate and predict the color of organic dyes (see the List of recent publications for more details). Our methodology takes into account the solvent effects as well as the pH impact on the color of the dyes. The theoretical tools used are the Density Functional Theory (DFT, for ground-state optimization) and the Time Dependent TDDFT for excitation spectra calculations. The solvent effects are taken into account via the PCM (Polarizable continuum Model).

Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin. The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work. The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-Z,syn configuration (in the inactive form of the protein) to C15-E,anti (in the active form). In this work, a reaction mechanism for this isomerization is proposed. DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied. Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.

In solution, the environment around the solute is determined solely by the solvent molecules, which are present closer to the solute. This interaction between solute and solvent shell is very crucial for equilibrium structure and reactivity of the solute. In the thesis, first we have investigated control of solvent polarity on the excited structure of 2,2,2 trifluroacetophenone and later effect of electronic excitation on the solvent shell organization has been described. It has been reported in literature that the lowest energy triplet configuration of 2,2,2 trifluroacetophenone corresponds to n,π* state. There are some other reports in favor of the probable existence of 2,2,2 trifluroacetophenone in n,π* lowest triplet state. Thus, transient absorption and time resolved resonance Raman spectroscopic methods have been used along with theoretical calculations to investigate the discrepancy in the assignment of the lowest triplet state configuration It has been observed that the lowest triplet state of 2,2,2 trifluroacetophenone is indeed nπ* and there is a solvent polarity induced change in triplet state energy ordering and structure changes. The absorption spectrum of hydrated electron is broad and structureless. So, it was though that the broadening feature could be attributed to homogeneous and inhomogeneous broadening. Transient resonance Raman spectrum of the water bending mode in presence of hydrated electron has been recorded at different excitation wavelengths. Interestingly, it has been observed that, peak position of water bending mode in presence of hydrated electron alters with change of excitation wavelength. A model has been proposed based on the experimental data.

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Made available in DSpace on 2014-10-09T12:46:25Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T13:57:21Z (GMT). No. of bitstreams: 1 07543.pdf: 4162108 bytes, checksum: fea345edb32c7ebb6b06110c513a47b1 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN/CNEN-SP / FAPESP:95/03214-1