Photoionization cross section calculations for the halogen-like ions Kr + and Xe +

Photoionization cross section calculations on the halogen-like ions; Kr + and Xe + have been performed for a photon energy range from each ion threshold to 15 eV, using large-scale close-coupling calculations within the Dirac--Coulomb R -matrix approximation. The results from our theoretical work are compared with recent measurements made at the ASTRID merged-beam set-up at the University of Aarhus in Denmark and from the Fourier transform ion cyclotron resonance trap method at the SOLEIL synchrotron radiation facility in Saint-Aubin, France Bizau et al (2011 J. Phys. B: At. Mol. Opt. Phys. 44 055205) and the advanced light source M{ü}ller (2012 private communication), Aguliar et al (2012 J. Phys.: Conf. Ser . at press). For each of these complex ions our theoretical cross section results over the photon energy range investigated are seen to be in excellent agreement with experiment. Resonance energy positions and quantum defects of the prominent Rydberg resonances series identified in the spectra are compared with experiment for these complex halogen-like ions.

Investigating the Implications of a Variable RBE on Proton Dose Fractionation Across a Clinical Pencil Beam Scanned Spread-Out Bragg Peak

Purpose: To investigate the clinical implications of a variable relative biological effectiveness (RBE) on proton dose fractionation. Using acute exposures, the current clinical adoption of a generic, constant cell killing RBE has been shown to underestimate the effect of the sharp increase in linear energy transfer (LET) in the distal regions of the spread-out Bragg peak (SOBP). However, experimental data for the impact of dose fractionation in such scenarios are still limited.

Methods and Materials: Human fibroblasts (AG01522) at 4 key depth positions on a clinical SOBP of maximum energy 219.65 MeV were subjected to various fractionation regimens with an interfraction period of 24 hours at Proton Therapy Center in Prague, Czech Republic. Cell killing RBE variations were measured using standard clonogenic assays and were further validated using Monte Carlo simulations and parameterized using a linear quadratic formalism.

Results: Significant variations in the cell killing RBE for fractionated exposures along the proton dose profile were observed. RBE increased sharply toward the distal position, corresponding to a reduction in cell sparing effectiveness of fractionated proton exposures at higher LET. The effect was more pronounced at smaller doses per fraction. Experimental survival fractions were adequately predicted using a linear quadratic formalism assuming full repair between fractions. Data were also used to validate a parameterized variable RBE model based on linear α parameter response with LET that showed considerable deviations from clinically predicted isoeffective fractionation regimens.

Conclusions: The RBE-weighted absorbed dose calculated using the clinically adopted generic RBE of 1.1 significantly underestimates the biological effective dose from variable RBE, particularly in fractionation regimens with low doses per fraction. Coupled with an increase in effective range in fractionated exposures, our study provides an RBE dataset that can be used by the modeling community for the optimization of fractionated proton therapy.

Lanthanide oxide nanotubes and nanorods: synthesis, processing, luminescence and catalytic properties

Esta tese relata estudos de síntese, caracterização da estrutura e das propriedades de fotoluminescência e aplicações de nanotubos e nanobastonetes de óxidos de lantanídeos em pontas para microscopia de força atómica, catálise heterogénea e compósitos de base polimérica. Há um interesse crescente em compreender como o confinamento quântico decorrente da redução do tamanho de partícula pode influenciar a eficiência da luminescência, a dinâmica dos estados excitados, a transferência de energia e os efeitos de termalização de nanoluminóforos. Em nanocristais dopados com lantanídeos (Ln3+), e apesar da localização dos estados 4f, ocorrem efeitos de confinamento quântico via interacção com os modos vibracionais da rede. Em particular, a termalização anómala, descrita para uma variedade de nanocristais dopados com Ln3+, tem sido atribuída à ausência de modos vibracionais de menor frequência. Este nanoconfinamento pode ter impacto na dinâmica da luminescência, bem como na transferência de energia mediada por modos vibracionais e processos de upconversion. Nesta tese, relata-se o estudo deste efeito em nanotubos de Gd2O3:Eu3+. A influência de parâmetros como a concentração de európio e as condições de calcinação também foi investigada. Algumas aplicações destes óxidos de lantanídeos também foram exploradas, nomeadamente a modificação de pontas usadas em microscopia de força atómica com nanobastonetes de Gd2O3:Eu3+, lograda através de dielectroforese, técnica que não degrada a emissão de luz (rendimento quântico 0.47). As pontas modificadas são estáveis sob condições de trabalho, podendo ser aplicadas, por exemplo, em microscopia óptica de varrimento de campo próximo (SNOM). A oxidação em fase líquida do etilbenzendo foi investigada usando como catalisador nanotubos de CeO2, em presença dos oxidantes hidroperóxido de t-butilo e H2O2, e do solvente acetonitrilo, e temperaturas entre 55 e 105 ºC. Nanobastonetes de Gd2O3:Eu3+ recobertos com sílica foram preparados pelo método sol-gel. Esta cobertura resultou num aumento, quer do rendimento quântico de emissão, de 0.51 para 0.86 (excitação a 255 nm), quer dos tempos de vida,de 1.43 para 1.80 ms (excitação a 394.4 nm). A superfície dos nanotubos cobertos com sílica foi modificada com o agente de acoplamento metacrilato de 3-(trimetoxissilil)propilo que permitiu a preparação de compósitos através da subsequente polimerização in-situ do estireno por técnicas de miniemulsão e solução. ABSTRACT: This thesis reports on the synthesis, characterisation of the structure and photoluminescence properties, and applications of nanotubes and nanorods of lanthanides oxides in atomic force microscopy tips, heterogeneous catalysis and polymer-base composites. There is a growing interest in understanding how size-dependent quantum confinement affects the photoluminescence efficiency, excited-state dynamics, energy-transfer and thermalisation phenomena in nanophosphors. For lanthanide (Ln3+)-doped nanocrystals, and despite the localisation of the 4f states, confinement effects are induced mostly via electron-phonon interactions. In particular, the anomalous thermalisation reported for a handful of Ln3+-doped nanocrystals has been rationalised by the absence of lowfrequency phonon modes. This nanoconfinement may further impact on the Ln3+ luminescence dynamics, such as phonon-assisted energy transfer or upconversion processes. Here, this effect is investigated in Gd2O3:Eu3+ nanotubes. The influence of parameters such as europium concentration and calcination procedure is also studied. Some applications of these lanthanides oxides have been explored, for instance the modification of atomic force microscopy tips with photoluminescent Gd2O3:Eu3+ nanorods, using dielectrophoresis, a technique which preserves the red emission of the nanorods (quantum yield 0.47). The modified tips are stable under working conditions and may find applications in scanning near-field optical microscopy. The liquid-phase oxidation of ethylbenzene over CeO2 nanotubes has been investigated, using tert-butyl-hydroperoxide and H2O2 as the oxidising agents, and acetonitrile as the solvent, in the range 55-105 ºC. Gd2O3:Eu3+ nanorods have been coated with silica via a sol-gel approach. The silica coating increases both, the Eu3+ absolute emission quantum yields from 0.51 to 0.86 (255 nm excitation), and decay times from 1.43 to 1.80 ms (394.4 nm excitation). The silica coating was modified with 3- (trimethoxysilyl) propyl methacrylate and, subsequently, composites have been prepared by in-situ radical polymerisation of styrene via miniemulsion and solution routes.

Polioxometalatos: dos agregados moleculares a redes e materiais

Esta dissertação teve como objectivo principal a preparação de novos materiais luminescentes contendo lantanopolioxometalatos. Foram utilizados polioxometalatos (POMs) do tipo Keggin, Wells-Dawson e [Ln(M5O18)2]9- com M (VI) = W, Mo contendo diferentes iões lantanídeo. Foram sintetizados materiais híbridos orgânico-inorgânicos com base em lantanopolioxometalatos e ligandos orgânicos. O efeito da coordenação destes ligandos orgânicos na luminescência dos iões lantanídeo (efeito de antena) foi investigado para os ácidos picolínico e 3-hidroxipicolínico. Os estudos de fotoluminescência destes materiais permitiram mostrar a existência de um processo de sensitização da emissão dos iões lantanídeo através de fenómenos de transferência de energia dos ligandos e do POM para o centro emissor. No caso particular dos materiais híbridos contendo POMs do tipo Wells-Dawson, a introdução do ligando orgânico levou à intensificação da absorção de energia através do POM, a qual era praticamente inexistente nos correspondentes lantanopolioxometalatos. Prepararam-se nanocompósitos do tipo “core/shell” contendo POMs e híbridos orgânico-inorgânicos como núcleo rodeados por uma camada de sílica. Os nanocompósitos preparados apresentam uma estrutura “core/shell” bem definida com um diâmetro médio de aproximadamente 35 nm. As técnicas de microscopia electrónica, nomeadamente o mapeamento por EDX, permitiram confirmar a presença dos POMs no núcleo das nanopartículas de sílica. A biofuncionalização destes nanocompósitos com um anticorpo foi estudada, com vista à potencial aplicação destes sistemas como biomarcadores ópticos. Os estudos de microscopia de fluorescência permitiram observar a emissão do Eu3+ presente nas nanopartículas biofuncionalizadas com o anticorpo, utilizando excitação na zona do ultravioleta. Estes resultados reforçam a viabilidade da aplicação destes sistemas como marcadores celulares em alternativa a “quantum dots” e corantes orgânicos. No âmbito dos nanomateriais, foi também preparado um material constituído por partículas de Na9[Eu(W5O18)2] de dimensões nanométricas, utilizando micelas invertidas como nanoreactores, de forma a limitar o tamanho das partículas. Foi realizada a preparação de novos materiais lamelares luminescentes por intercalação de POMs e respectivos materiais híbridos em argilas aniónicas de zinco e alumínio. A intercalação foi realizada através de um método de troca aniónica directa usando uma argila contendo nitrato como anião precursor. O estudo por difracção de raios-X revelou-se uma técnica fundamental na caracterização destes materiais, nomeadamente através da determinação da altura de galeria. A partir deste parâmetro foi possível verificar a orientação da espécie intercalada na argila. No caso da intercalação do anião do tipo Keggin, o estudo por RMN de 31P MAS permitiu identificar a espécie intercalada na argila. As propriedades de luminescência foram estudadas para a generalidade dos novos materiais preparados.

Contribution to fundamental aspects of biophysics, radiobiology, and modeling of cellular response to low radiation doses

Tese de doutoramento, Engenharia Biomédica e Biofísica, Universidade de Lisboa, Faculdade de Ciências, 2014

An investigation into the functional role of the D1:1 and D1:2 polypeptides in photosystem II in cyanobacteria : the effect of changing PSI/PSII ratio on photoinhibition in Synechococcus sp. PCC7942 /

The cyanobacterium Synechococcus sp. PCC 7942 (Anacystis nidulans R2) adjusts its photosynthetic function by changing one of the polypeptides of photosystem II. This polypeptide, called Dl, is found in two forms in Synechococcus sp. PCC 7942. Changing the growth light conditions by increasing the light intensity to higher levels results in replacement of the original form of D 1 polypeptide, D 1: 1, with another form, D 1 :2. We investigated the role of these two polypeptides in two mutant strains, R2S2C3 (only Dl:l present) and R2Kl (only Dl:2 present) In cells with either high or low PSI/PSII. R2S2C3 cells had a lower amplitude for 77 K fluorescence emission at 695 nm than R2Kl cells. Picosecond fluorescence decay kinetics showed that R2S2C3 cells had shorter lifetimes than R2Kl cells. The lower yields and shorter lifetimes observed in the D 1 and Dl:2 containing cells. containing cells suggest that the presence of D 1: 1 results in more photochemical or non-photochemical quenching of excitation energy In PSII. One of the most likely mechanisms for the increased quenching in R2S2C3 cells could be an increased efficiency in the transfer of excitation energy from PSII to PSI. However, photophysical studies including 77 K fluorescence measurements and picosecond time resolved decay kinetics comparing low and high PSI/PSII cells did not support the hypothesis that D 1: 1 facilitates the dissipation of excess energy by energy transfer from PSII to PSI. In addition physiological studies of oxygen evolution measurements after photoinhibition treatments showed that the two mutant cells had no difference in their susceptibility to photoinhibition with either high PSI/PSII ratio or low PSI/PSII ratio. Again suggesting that, the energy transfer efficiency from PSII to PSI is likely not a factor in the differences between Dl:l and Dl:2 containing cells.

Heterogeneity of photosystem II as it occurs in domain specific regions of the thylakoid membrane of spinach (spinacia oleracia L.)

Thylakoid membrane fractions were prepared from specific regions of thylakoid membranes of spinach (Spinacia oleracea). These fractions, which include grana (83), stroma (T3), grana core (8S), margins (Ma) and purified stroma (Y100) were prepared using a non-detergent method including a mild sonication and aqueous two-phase partitioning. The significance of PSlla and PSII~ centres have been described extensively in the literature. Previous work has characterized two types of PSII centres which are proposed to exist in different regions of the thylakoid membrane. a-centres are suggested to aggregate in stacked regions of grana whereas ~-centres are located in unstacked regions of stroma lamellae. The goal of this study is to characterize photosystem II from the isolated membrane vesicles representing different regions of the higher plant thylakoid membrane. The low temperature absorption spectra have been deconvoluted via Gaussian decomposition to estimate the relative sub-components that contribute to each fractions signature absorption spectrum. The relative sizes of the functional PSII antenna and the fluorescence induction kinetics were measured and used to determine the relative contributions of PSlla and PSII~ to each fraction. Picosecond chlorophyll fluorescence decay kinetics were collected for each fraction to characterize and gain insight into excitation energy transfer and primary electron transport in PSlla and PSII~ centres. The results presented here clearly illustrate the widely held notions of PSII/PS·I and PSlIa/PSII~ spatial separation. This study suggests that chlorophyll fluorescence decay lifetimes of PSII~ centres are shorter than those of PSlIa centres and, at FM, the longer lived of the two PSII components renders a larger yield in PSlIa-rich fractions, but smaller in PSIlr3-rich fractions.

Localization of the mechanism of pH-dependent non- photochemical fluorescence quenching in thylakoid membranes

Higher plants have evolved a well-conserved set of photoprotective mechanisms, collectively designated Non-Photochemical Quenching of chlorophyll fluorescence (qN), to deal with the inhibitory absorption of excess light energy by the photosystems. Their main contribution originates from safe thermal deactivation of excited states promoted by a highly-energized thylakoid membrane, detected via lumen acidification. The precise origins of this energy- or LlpH-dependent quenching (qE), arising from either decreased energy transfer efficiency in PSII antennae (~ Young & Frank, 1996; Gilmore & Yamamoto, 1992; Ruban et aI., 1992), from alternative electron transfer pathways in PSII reaction centres (~ Schreiber & Neubauer, 1990; Thompson &Brudvig, 1988; Klimov et aI., 1977), or from both (Wagner et aI., 1996; Walters & Horton, 1993), are a source of considerable controversy. In this study, the origins of qE were investigated in spinach thylakoids using a combination of fluorescence spectroscopic techniques: Pulse Amplitude Modulated (PAM) fluorimetry, pump-probe fluorimetry for the measurement of PSII absorption crosssections, and picosecond fluorescence decay curves fit to a kinetic model for PSII. Quenching by qE (,..,600/0 of maximal fluorescence, Fm) was light-induced in circulating samples and the resulting pH gradient maintained during a dark delay by the lumenacidifying capabilities of thylakoid membrane H+ ATPases. Results for qE were compared to those for the addition of a known antenna quencher, 5-hydroxy-1,4naphthoquinone (5-0H-NQ), titrated to achieve the same degree of Fm quenching as for qE. Quenching of the minimal fluorescence yield, F0' was clear (8 to 130/0) during formation of qE, indicative of classical antenna quenching (Butler, 1984), although the degree was significantly less than that achieved by addition of 5-0H-NQ. Although qE induction resulted in an overall increase in absorption cross-section, unlike the decrease expected for antenna quenchers like the quinone, a larger increase in crosssection was observed when qE induction was attempted in thylakoids with collapsed pH gradients (uncoupled by nigericin), in the absence of xanthophyll cycle operation (inhibited by DTT), or in the absence of quenching (LlpH not maintained in the dark due to omission of ATP). Fluorescence decay curves exhibited a similar disparity between qE-quenched and 5-0H-NQ-quenched thylakoids, although both sets showed accelerated kinetics in the fastest decay components at both F0 and Fm. In addition, the kinetics of dark-adapted thylakoids were nearly identical to those in qEquenched samples at F0' both accelerated in comparison with thylakoids in which the redox poise of the Oxygen-Evolving Complex was randomized by exposure to low levels of background light (which allowed appropriate comparison with F0 yields from quenched samples). When modelled with the Reversible Radical Pair model for PSII (Schatz et aI., 1988), quinone quenching could be sufficiently described by increasing only the rate constant for decay in the antenna (as in Vasil'ev et aI., 1998), whereas modelling of data from qE-quenched thylakoids required changes in both the antenna rate constant and in rate constants for the reaction centre. The clear differences between qE and 5-0H-NQ quenching demonstrated that qE could not have its origins in the antenna alone, but is rather accompanied by reaction centre quenching. Defined mechanisms of reaction centre quenching are discussed, also in relation to the observed post-quenching depression in Fm associated with photoinhibition.

The measurement of the optical absorption cross section of photosystem 1 and photosystem 2 from whole live cells of porphyridium cruentum, in light state 1 and light state 2

The optical cross section of PS I in whole cells of Porphyridium cruentum (UTEX 161), held in either state 1 or state 2, was determined by measuring the change in absorbance at 820nm, an indication of P700+; the X-section of PS2 was determined by measuring the variable fluorescence, (Fv-Fo)/Fo, from PS2. Both cross-sections were 7 determined by fitting Poisson distribution equations to the light saturation curves obtained with single turnover laser flashes which varied in intensity from zero to a level where maximum yield occurred. Flash wavelengths of 574nm, 626nm, and 668nm were used, energy absorbed by PBS, by PBS and chla, and by chla respectively. There were two populations of both PSi and PS2. A fraction of PSi is associated with PBS, and a fraction of PS2 is free from PBS. On the transition S1->S2, only with PBS-absorbed energy (574nm) did the average X-section of PSi increase (27%), and that of PS2 decrease (40%). The fraction of PSi associated with PBS decreased, from 0.65 to 0.35, and the Xsection of this associated PS 1 increased, from 135±65 A2 to 400±300A2. The cross section of PS2 associated with PBS decreased from 150±50 A2 to 85±45 A2, but the fraction of PS2 associated with PBS, approximately 0.75, did not change significantly. The increase in PSi cross section could not be completely accounted for by postulating that several PSi are associated with a single PBS and that in the transition to state2, fewer PSi share the same number of PBS, resulting in a larger X-section. It is postulated that small changes occur in the attachment of PS2 to PBS causing energy to be diverted to the attached PSi. These experiments support neither the mobile-PBS model of state transitions nor that of spillover. From cross section changes there was no evidence of energy transfer from PS2 to PSi with 668nm light. The decrease in PS2 fluorescence which occurred at this wavelength cannot be explained by energy transfer; another explanation must be sought. No explanation was found for an observed decrease in PSi yield at high flash intensities.

Effect of pH on non-photochemical quenching in spinach photsystem 2 particles as measured by picosecond fluorescence decay kinetics

Single photon timing was used to study picosecond chlorophyll a fluorescence decay kinetics of pH induced non-photochemical quenching in spinach photosystem 2 particles. The characteristics of this quenching are a decrease in chlorophyll a fluorescence yield as well as a decrease in photochemistry at low pH. Picosecond kinetics of room temperature fluorescence temporally resolve the individual components of the steady state fluorescence yield into components that are related to primary energy conversion processes in photosystem 2. Four components were resolved for dark adapted (Fo), light saturated (Fm), and chemically reduced (Nadithionite) photosystem 2 reaction centres. The fastest and slowest components, indicative of energy transfer to and energy capture by the photosystem 2 reaction centre and uncoupled ("dead") chlorophyll, respectively, were not affected by changing pH from 6.5 to 4.0. The two intermediate components, indicative of electron transfer processes within the reaction centre of photosystem 2, were affected by the pH change. Results indicate that the decrease in the steady state fluorescence yield at low pH was primarily due to the decrease in lifetime and amplitude of the slower of the intermediate components. These results imply that the decrease in steady state fluorescence yield at low pH is not due to changes in energy transfer to and energy capture by the photosystem 2 reaction centre, but is related to changes in charge stabilization and charge recombination in the photosystem 2 reaction centre.

Competing demands for a complex system : photosystem II repair, photoprotection and quantum yield

Photosynthesis in general is a key biological process on Earth and Photo system II (PSII) is an important component of this process. PSII is the only enzyme capable of oxidizing water and is largely responsible for the primordial build-up and present maintenance of the oxygen in the atmosphere. This thesis endeavoured to understand the link between structure and function in PSII with special focus on primary photochemistry, repair/photodamage and spectral characteristics. The deletion of the PsbU subunit ofPSII in cyanobacteria caused a decoupling of the Phycobilisomes (PBS) from PSII, likely as a result of increased rates of PSII photodamage with the PBS decoupling acting as a measure to protect PSII from further damage. Isolated fractions of spinach thylakoid membranes were utilized to characterize the heterogeneity present in the various compartments of the thylakoid membrane. It was found that the pooled PSIILHCII pigment populations were connected in the grana stack and there was also a progressive decrease in the reaction rates of primary photochemistry and antennae size of PSII as the sample origin moved from grana to stroma. The results were consistent with PSII complexes becoming damaged in the grana and being sent to the stroma for repair. The dramatic quenching of variable fluorescence and overall fluorescent yield of PSII in desiccated lichens was also studied in order to investigate the mechanism by which the quenching operated. It was determined that the source of the quenching was a novel long wavelength emitting external quencher. Point mutations to amino acids acting as ligands to chromophores of interest in PSII were utilized in cyanobacteria to determine the role of specific chromophores in energy transfer and primary photochemistry. These results indicated that the Hl14 ligated chlorophyll acts as the 'trap' chlorophyll in CP47 at low temperature and that the Q130E mutation imparts considerable changes to PSII electron transfer kinetics, essentially protecting the complex via increased non-radiative charge Photosynthesis in general is a key biological process on Earth and Photo system II (PSII) is an important component of this process. PSII is the only enzyme capable of oxidizing water and is largely responsible for the primordial build-up and present maintenance of the oxygen in the atmosphere. This thesis endeavoured to understand the link between structure and function in PSII with special focus on primary photochemistry, repair/photodamage and spectral characteristics. The deletion of the PsbU subunit ofPSII in cyanobacteria caused a decoupling of the Phycobilisomes (PBS) from PSII, likely as a result of increased rates of PSII photodamage with the PBS decoupling acting as a measure to protect PSII from further damage. Isolated fractions of spinach thylakoid membranes were utilized to characterize the heterogeneity present in the various compartments of the thylakoid membrane. It was found that the pooled PSIILHCII pigment populations were connected in the grana stack and there was also a progressive decrease in the reaction rates of primary photochemistry and antennae size of PSII as the sample origin moved from grana to stroma. The results were consistent with PSII complexes becoming damaged in the grana and being sent to the stroma for repair. The dramatic quenching of variable fluorescence and overall fluorescent yield of PSII in desiccated lichens was also studied in order to investigate the mechanism by which the quenching operated. It was determined that the source of the quenching was a novel long wavelength emitting external quencher. Point mutations to amino acids acting as ligands to chromophores of interest in PSII were utilized in cyanobacteria to determine the role of specific chromophores in energy transfer and primary photochemistry. These results indicated that the Hl14 ligated chlorophyll acts as the 'trap' chlorophyll in CP47 at low temperature and that the Q130E mutation imparts considerable changes to PSII electron transfer kinetics, essentially protecting the complex via increased non-radiative charge.

The Fast Regulation of Photosynthesis in Diatoms: an inquiry into the physiological and physical origins of non-photochemical chlorophyll fluorescence quenching.

Diatoms are renowned for their robust ability to perform NPQ (Non-Photochemical Quenching of chlorophyll fluorescence) as a dissipative response to heightened light stress on photosystem II, plausibly explaining their dominance over other algal groups in turbulent light environs. Their NPQ mechanism has been principally attributed to a xanthophyll cycle involving the lumenal pH regulated reversible de-epoxidation of diadinoxanthin. The principal goal of this dissertation is to reveal the physiological and physical origins and consequences of the NPQ response in diatoms during short-term transitions to excessive irradiation. The investigation involves diatom species from different originating light environs to highlight the diversity of diatom NPQ and to facilitate the detection of core mechanisms common among the diatoms as a group. A chiefly spectroscopic approach was used to investigate NPQ in diatom cells. Prime methodologies include: the real time monitoring of PSII excitation and de-excitation pathways via PAM fluorometry and pigment interconversion via transient absorbance measurements, the collection of cryogenic absorbance spectra to measure pigment energy levels, and the collection of cryogenic fluorescence spectra and room temperature picosecond time resolved fluorescence decay spectra to study excitation energy transfer and dissipation. Chemical inhibitors that target the trans-thylakoid pH gradient, the enzyme responsible for diadinoxanthin de-epoxidation, and photosynthetic electron flow were additionally used to experimentally manipulate the NPQ response. Multifaceted analyses of the NPQ responses from two previously un-photosynthetically characterised species, Nitzschia curvilineata and Navicula sp., were used to identify an excitation pressure relief ‘strategy’ for each species. Three key areas of NPQ were examined: (i) the NPQ activation/deactivation processes, (ii) how NPQ affects the collection, dissipation, and usage of absorbed light energy, and (iii) the interdependence of NPQ and photosynthetic electron flow. It was found that Nitzschia cells regulate excitation pressure via performing a high amplitude, reversible antenna based quenching which is dependent on the de-epoxidation of diadinoxanthin. In Navicula cells excitation pressure could be effectively regulated solely within the PSII reaction centre, whilst antenna based, diadinoxanthin de-epoxidation dependent quenching was implicated to be used as a supplemental, long-lasting source of excitation energy dissipation. These strategies for excitation balance were discussed in the context of resource partitioning under these species’ originating light climates. A more detailed investigation of the NPQ response in Nitzschia was used to develop a comprehensive model describing the mechanism for antenna centred non-photochemical quenching in this species. The experimental evidence was strongly supportive of a mechanism whereby: an acidic lumen triggers the diadinoxanthin de-epoxidation and protonation mediated aggregation of light harvesting complexes leading to the formation of quencher chlorophyll a-chlorophyll a dimers with short-lived excited states; quenching relaxes when a rise in lumen pH triggers the dispersal of light harvesting complex aggregates via deprotonation events and the input of diadinoxanthin. This model may also be applicable for describing antenna based NPQ in other diatom species.

Optimizing Computational Frameworks to Study the Influence of the Protein Environment on the Individual Site Energies of Chromophores in Photosystem II of Photosynthesis

Photosynthesis is a process in which electromagnetic radiation is converted into chemical energy. Photosystems capture photons with chromophores and transfer their energy to reaction centers using chromophores as a medium. In the reaction center, the excitation energy is used to perform chemical reactions. Knowledge of chromophore site energies is crucial to the understanding of excitation energy transfer pathways in photosystems and the ability to compute the site energies in a fast and accurate manner is mandatory for investigating how protein dynamics ef-fect the site energies and ultimately energy pathways with time. In this work we developed two software frameworks designed to optimize the calculations of chro-mophore site energies within a protein environment. The first is for performing quantum mechanical energy optimizations on molecules and the second is for com-puting site energies of chromophores in a fast and accurate manner using the polar-izability embedding method. The two frameworks allow for the fast and accurate calculation of chromophore site energies within proteins, ultimately allowing for the effect of protein dynamics on energy pathways to be studied. We use these frame-works to compute the site energies of the eight chromophores in the reaction center of photosystem II (PSII) using a 1.9 Å resolution x-ray structure of photosystem II. We compare our results to conflicting experimental data obtained from both isolat-ed intact PSII core preparations and the minimal reaction center preparation of PSII, and find our work more supportive of the former.

Ligand Design for Dual Property Single Molecule Magnets

This thesis describes two different approaches for the preparation of polynuclear clusters with interesting structural, magnetic and optical properties. Firstly, exploiting p-tert-butylcalix[4]arene (TBC4) macrocycles together with selected Ln(III) ions for the assembly of emissive single molecule magnets, and secondly the preparation and coordination of a chiral mpmH ligand with selected 3d transition metal ions, working towards the discovery of chiral polynuclear clusters. In Project 1, the coordination chemistry of the TBC4 macrocycle together with Dy(III) and Tb(III) afforded two Ln6[TBC4]2 complexes that have been structurally, magnetically and optically characterized. X-ray diffraction studies reveal that both complexes contain an octahedral core of Ln6 ions capped by two fully deprotonated TBC4 macrocycles. Although the unit cells of the two complexes are very similar, the coordination geometries of their Ln(III) ions are subtly different. Variable temperature ac magnetic susceptibility studies reveal that both complexes display single molecule magnet (SMM) behaviour in zero dc field and the energy barriers and associated pre-exponential factors for each relaxation process have been determined. Low temperature solid state photoluminescence studies reveal that both complexes are emissive; however, the f-f transitions within the Dy6 complex were masked by broad emissions from the TBC4 ligand. In contrast, the Tb(III) complex displayed green emission with the spectrum comprising four sharp bands corresponding to 5D4 → 7FJ transitions (where J = 3, 4, 5 and 6), highlighting that energy transfer from the TBC4 macrocycle to the Tb(III) ion is more effective than to Dy. Examples of zero field Tb(III) SMMs are scarce in the chemical literature and the Tb6[TBC4]2 complex represents the first example of a Tb(III) dual property SMM assembled from a p-tert-butylcalix[4]arene macrocycle with two magnetically derived energy barriers, Ueff of 79 and 63 K. In Project 2, the coordination of both enantiomers of the chiral ligand, α-methyl-2-pyridinemethanol (mpmH) to Ni(II) and Co(II) afforded three polynuclear clusters that have been structurally and magnetically characterized. The first complex, a Ni4 cluster of stoichiometry [Ni4(O2CCMe3)4(mpm)4]·H2O crystallizes in a distorted cubane topology that is well known in Ni(II) cluster chemistry. The final two Co(II) complexes crystallize as a linear mixed valence trimer with stoichiometry [Co3(mpm)6]·(ClO4)2, and a Co4 mixed valence complex [Co(II)¬2Co(III)2(NO3)2(μ-mpm)4(ONO2)2], whose structural topology resembles that of a defective double cubane. All three complexes crystallize in chiral space groups and circular dichroism experiments further confirm that the chirality of the ligand has been transferred to the respective coordination complex. Magnetic susceptibility studies reveal that for all three complexes, there are competing ferro- and antiferromagnetic exchange interactions. The [Co(II)¬2Co(III)2(NO3)2(μ-mpm)4(ONO2)2] complex represents the first example of a chiral mixed valence Co4 cluster with a defective double cubane topology.

Polyoxométallates hybrides : vers des systèmes covalents photoactifs dans le visible

Réalisé en cotutelle, sous la direction du Pr. Bernold Hasenknopf, à l'Institut Parisien de Chimie Moléculaire, Université Pierre et Marie Curie (Paris VI, France) et dans le cadre de l'Ecole Doctorale "Physique et Chimie des Matériaux" - Spécialité Chimie Inorganique (ED397).