Les membranes impliquées dans les processus bioénergétiques arborent une très grande densité de protéines, paramètre déterminant pour leur organisation supra-moléculaire. Dans ce travail, nous avons utilisé la bactérie thermophile Geobacillus stearothermophilus comme modèle pour étudier la formation de super-complexes de protéines membranaires, en vue d'une étude structurale. Nous avons purifié et caractérisé un super-complexe comprenant une menaquinol: cytochrome c oxydoréductase (b6c), un cytochrome c550 et une cytochrome c oxydase caa3. En combinant des titrations par spectroscopie optique et résonance paramagnétique électronique, nous avons pu déterminer les potentiels d'oxydo-réduction de la plupart des cofacteurs et combler ainsi une lacune dans l'étude des chaînes de transfert d'électrons utilisant des quinones à bas potentiel redox, les ménaquinones. Nous avons ainsi montré que les potentiels redox des cofacteurs du cytochrome b6c terminés par celui des quinones. Ce travail va à l'encontre de données partielles antérieures publiées, mais est en parfait accord avec les modèles du Q-cycle de Peter Mitchell. Les résultats obtenus ont des répercussions sur les rendements bioénergétiques des différents maillons de la chaîne de transfert. / Bioenergetic membranes present a high protein density - a crucial factor for their organizationinto super-complexes. This project uses the thermophilic bacteria Geobacillus stearothermophilusas a model to study the formation of membrane protein super-complexes with the aim of structuralstudies. We purified and characterized a super-complex between a menaquinone : cytochromec oxidoreductase (b6c), a cytochrome c550, and a cytochrome c oxidase caa3. Using both opticaland EPR spectroscopy methods, we performed the redox titrations of most of the redox cofactorsof the super-complex. Thus, these results enable a new understanding of menaquinone-usingelectron transport chains, showing that quinones’ redox potential determines the redox potentialof the cytochrome b6c’s cofactors. The conclusions differ from previous partial data, althoughthey fit perfectly with Peter Mitchell’s model of the Q-cycle. These unexpected redox potentialsimpact bioenergetic yields at different levels of the electron transfer chain.

Reductive electron transfer has been successfully utilized to facilitate the first enantioselective desymmetrisation of malonate derivatives. Selective monoreduction of cyclic 1,3-diesters through the combined use of SmI2-Et3N and chiral non-racemic diols has granted rapid access to enantioenriched β-hydroxy acids containing challenging quaternary centres – an abundant motif in many drug molecules. Unique radical anions generated from the single electron reduction of cyclic 1,3-diesters have been exploited in cyclisation cascades. Capture of acyl-type radical anions by both alkene and alkyne acceptors have permitted the construction of complex bicyclic architectures in a single synthetic operation. The reductive cyclisation cascade of lactones has also been demonstrated, using SmI2-H2O to achieve a challenging domino 5-exo-trig/6-exo-trig cyclisation event. This process generates highly decorated carbo[5.4.0]bicyclic scaffolds with complete diastereocontrol.

L'interaction de particules énergétiques avec les résultats de l'eau dans l'excitation et l'ionisation des molécules d'eau. Le processus d'ionisation se rapporte à la génération de l'excès d'électrons détachés de leurs molécules parentes et laissant derrière le trou positive (notée H₂O•⁺). Cela se produit sur le calendrier d'une transition électronique ~ 10⁻¹⁵s. Les processus chimiques plus anciens de H₂O•⁺ et l'excès d'électrons vers autre question suivie de l'eau en vrac ionisants restent encore peu par rapport connu et constitue un sujet difficile dans la chimie de rayonnement. Dans ma thèse, les techniques de radiolyse d'impulsions picoseconde ont été utilisés pour observer la cinétique de la SO₄•⁻, H₂PO₄• dans de l'acide sulfurique très concentré et solutions d'acide phosphorique sur une large gamme de concentrations (de 1 mol L⁻¹ à l'acide pur). Les résultats expérimentaux montrent clairement que le radical secondaire de sulfurique (SO₄•⁻) et de l'acide phosphorique (H₂PO₄•) peuvent être formés par l'intermédiaire de deux mécanismes : détachement d'électrons direct par l'impulsion d'électrons (7 ps) et le transfert d'électrons ultra-rapide des solutés au radical cation de l'eau H₂O•⁺. La réactivité des espèces oxydantes fortes, H₂O•⁺ vers les solutés dans des solutions aqueuses très concentrées est quantitativement démontré. / The interaction of energetic particles with water results in the excitation and ionization of water molecules. The ionization process refers to the generation of the excess electrons detached from their parent molecules and leaving behind the positive hole (denoted as H₂O•⁺). This occurs on the timescale of an electronic transition ~10⁻¹⁵ s. The earliest chemical processes of H₂O•⁺ and excess electron towards other matter followed water ionizing in bulk still remain relative little known and constitute a challenging subject in radiation chemistry. In my thesis, picosecond pulse radiolysis techniques were used to observe the kinetics of the SO₄•⁻, H₂PO₄• in highly concentrated sulfuric acid and phosphoric acid solutions over a large range of concentrations (from 1 mol L⁻¹ to neat acid). The experimental results showed clearly that the secondary radical of sulfuric (SO₄•⁻) and phosphoric acid (H₂PO₄•) can be formed via two mechanisms: direct electron detachment by the electron pulse (7 ps) and ultrafast electron transfer from the solutes to the radical cation of water H₂O•⁺. The reactivity of the strongest oxidizing species, H₂O•⁺ towards the solutes in highly concentrated aqueous solutions is quantitatively demonstrated.

abstract: Chemical modification of (semi)conducting surfaces with soft-material coatings containing electrocatalysts provides a strategy for developing integrated constructs that capture, convert, and store solar energy as fuels. However, a lack of effective strategies for interfacing electrocatalysts with solid-state materials, and an incomplete understanding of performance limiting factors, inhibit further development. In this work, chemical modification of a nanostructured transparent conductive oxide, and the III-V semiconductor, gallium phosphide, is achieved by applying a thin-film polymer coating containing appropriate functional groups to direct, template, and assemble molecular cobalt catalysts for activating fuel-forming reactions. The heterogeneous-homogeneous conducting assemblies enable comparisons of the structural and electrochemical properties of these materials with their homogeneous electrocatalytic counterparts. For these hybrid constructs, rational design of the local soft-material environment yields a nearly one-volt span in the redox chemistry of the cobalt metal centers. Further, assessment of the interplay between light absorption, charge transfer, and catalytic activity in studies involving molecular-catalyst-modified semiconductors affords models to describe the rates of photoelectrosynthetic fuel production as a function of the steady-state concentration of catalysts present in their activated form. These models provide a conceptual framework for extracting kinetic and thermodynamic benchmarking parameters. Finally, investigation of molecular ‘proton wires’ inspired by the Tyrosine Z-Histidine 190 redox pair in Photosystem II, provides insight into fundamental principles governing proton-coupled electron transfer, a process essential to all fuel-forming reactions relevant to solar fuel generation. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2020

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21836号 / 農博第2349号 / 新制||農||1068(附属図書館) / 学位論文||H31||N5208(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 加納 健司, 教授 三芳 秀人, 教授 三上 文三 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22459号 / 工博第4720号 / 新制||工||1737(附属図書館) / 京都大学大学院工学研究科物質エネルギー化学専攻 / (主査)教授 作花 哲夫, 教授 安部 武志, 教授 阿部 竜 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

The efficiency of photoconversion systems, such as organic photovoltaic (OPV) cells, is largely controlled by a series of fundamental photophysical processes occurring at the interface before carrier collection. A profound understanding of ultrafast interfacial charge transfer (CT), charge separation (CS), and charge recombination (CR) is the key determinant to improving the overall performances of photovoltaic devices. The discussion in this dissertation primarily focuses on the relevant parameters that are involved in photon absorption, exciton separation, carrier transport, carrier recombination and carrier collection in organic photovoltaic devices. A combination of steady-state and femtosecond broadband transient spectroscopies was used to investigate the photoinduced charge carrier dynamics in various donor-acceptor systems. Furthermore, this study was extended to investigate some important factors that influence charge transfer in donor-acceptor systems, such as the morphology, energy band alignment, electronic properties and chemical structure. Interestingly, clear correlations among the steady-state measurements, time-resolved spectroscopy results, grain alignment of the electron transporting layer (ETL), carrier mobility, and device performance are found. In this thesis, we explored the significant impacts of ultrafast charge separation and charge recombination at donor/acceptor (D/A) interfaces on the performance of a conjugated polymer PTB7-Th device with three fullerene acceptors: PC71BM, PC61BM and IC60BA. Time-resolved laser spectroscopy and high-resolution electron microscopy can illustrate the basis for fabricating solar cell devices with improved performances. In addition, we studied the effects of the incorporation of heavy metals into π-conjugated chromophores on electron transfer by monitoring the triplet state lifetime of the oligomer using transient absorption spectroscopy, as understanding the mechanisms controlling intersystem crossing and photoinduced electron transfer dynamics is required to improve the device performance of solar cells. Here, we evaluated the effects of incorporating Pt(II) on intersystem crossing and photoinduced electron transfer by comparing and analyzing the photoexcited dynamics of DPP-Pt(II)(acac) and metal-free DPP with different acceptors such as TCNE, TMPyP, and TPyP.

Anaerobic ammonium oxidation (anammox) by anammox bacteria contributes significantly to the global nitrogen cycle and plays a major role in sustainable wastewater treatment. To date, autotrophic nitrogen removal by anammox bacteria is the most efficient and environmentally friendly process for the treatment of ammonium in wastewaters; its application can save up to 60% of the energy input, nearly 100% elimination of carbon demand and 80% decrease in excess sludge compared to conventional nitrification/denitrification process. In the anammox process, ammonium (NH4+) is directly oxidized to dinitrogen gas (N2) using intracellular electron acceptors such as nitrite (NO2–) or nitric oxide (NO). In the absence of NO2– or NO, anammox bacteria can couple formate oxidation to the reduction of metal oxides such as Fe(III) or Mn(IV). Their genomes contain homologs of Geobacter and Shewanella cytochromes involved in extracellular electron transfer (EET). However, it is still unknown whether anammox bacteria have EET capability and can couple the oxidation of NH4+ with transfer of electrons to extracellular electron acceptors. In this dissertation, I discovered by using complementary approaches that in the absence of NO2–, freshwater and marine anammox bacteria couple the oxidation of NH4+ with transfer of electrons to carbon-based insoluble extracellular electron acceptors such as graphene oxide (GO) or electrodes poised at a certain potential in microbial electrolysis cells (MECs). Metagenomics, fluorescence in-situ hybridization and electrochemical analyses coupled with MEC performance confirmed that anammox electrode biofilms were responsible for current generation through EET-dependent oxidation of NH4+. 15N-labelling experiments revealed the molecular mechanism of the EET-dependent anammox process. NH4+ was oxidized to N2 via hydroxylamine (NH2OH) as intermediate when electrode was used as the terminal electron acceptor. Comparative transcriptomics analysis supported isotope labelling experiments and revealed an alternative pathway for NH4+ oxidation coupled to EET when electrode was used as electron acceptor. The results presented in my dissertation provide the first experimental evidence that marine and freshwater anammox bacteria can couple NH4+ oxidation with EET, which is a significant breakthrough that is promising in the context of implementing EET-dependent anammox process for energy-efficient treatment of nitrogen using bioelectrochemical systems.

Microbial fuel cell (MFC) technology is a renewable energy source that employs microorganisms as biocatalysts to degrade substrates into electrons and protons, and then transfer the electrons to the anode electrode. Electron transfer rates by microorganisms depend on many factors as well as on their diverse electron transfer mechanisms. The present study compared cytochromes, flavoproteins, electron transfer complexes, redoxins and other extracellular membrane proteins that have direct involvement in electron transfer mechanisms in Escherichia coli str. K-12 MG1655, Rhodopseudomonas pulastris DX-1 and Shewanella oneidensis MR-1. Escherichia coli str. The results showed that K-12 MG1655 had a more diverse range of extracellular proteins for electron transfer mechanisms compared to Rhodopseudomonas pulastris DX-1 and Shewanella oneidensis MR-1. Escherichia coli str. K-12 MG1655 expressed more flavoproteins, redoxin and electron transfer complex related proteins that had direct involvement in electron transfer mechanisms compared to two other bacterial species indicating that it may be able to transfer more electrons when employed in MFC technique. Escherichia coli str. K-12 MG1655 expressed 16 cytochromes, 9 flavoproteins, 6 redoxins, 6 electron transport complexes, 1 hypothetical and 1 oxidoreductase proteins. On the other hand, Rhodopseudomonas pulastris DX-1 and Shewanella oneidensis MR-1 expressed 26 and 35 cytochromes proteins. But these two bacterial species expressed less flavoproteins and redoxin related proteins and they didn’t express any electron transport complexes or hypothetical and oxidoreductase related proteins for electron transfer. STRING and SMART results suggested that the identified proteins transferred electrons either by connecting with other types of identified proteins in the constructed gene network or independently by taking part in oxidation-reduction reaction, metal ion reduction reaction or by their FMN binding activities.

The potential antimalarial and anticancer effect of molecules containing 1,10-phenanthroline skeleton has been suspected on several previous studies. It is why the goal of this project is to synthesize novel 1,10-phenanthrolines and cyclic analogs. The originality of this project is the synthesis way of these novel compounds. Indeed, these structures will be obtained through an original redox approach developed in the SMITH laboratory using the tetrakis(dimethylamino)ethylene (TDAE) reagent.      The TDAE is an electron rich organic molecule which is an effective reducing agent capable of generating an anion from halogenated derivatives under mild conditions via a single electron transfer (SET). From the different substrate we will work with, the TDAE will generate an anion which will be additioned on the 1,10-phenanthroline-5,6-dione. These different substrates will be aromatic and heterocyclic nitro-benzylic, and quinonic derivates as well as bromodifluoromethyl heteroarylated substrates. A one pot two step (reduction, dehydration) reaction will be done on these addition products, in order to obtain a cyclised product.        It is the first time we try these reactions on these kind on molecules, it is why this project needs a lot of optimization and that the yield obtained are medium or equal to zero. However, we observed that the addition reaction with TDAE worked with 4 substrates out of 6. We tried the cyclisation reaction on only one addition product and we think that after some improvement of the reaction conditions and the work-up, we will be able to obtain the product with a good yield. / Tidigare studier har indikerat att molekyler med 1,10-phenanthrolineskelett har en skyddande effekt mot malaria och cancer. Syftet med detta projekt är att syntetisera nya 1,10-phenanthrolinar och cykliska analoger. Framställningsmetoden som användes i denna studie har inte undersökts tidigare.    Föreningen skapades genom en originalmetod utnyttjande en redoxreaktion med hjälp av en TDAE-reagens. TDAE är en elektronrik organisk molekyl och fungerar som en effektiv reduktionsagent. Med hjälp av en enelektronöverföring (SET) kan en anjon framställas under milda förhållanden utifrån halogena derivat. Anjonen tillförs 1,10-phenanthroline-5,6-dione. De olika substraten är heteroaromatiska nitro-benzyliska och quinoniska derivat, samt bromodifluorometylheteroarylerade. Cykliska produkter erhölls genom en tvåstegsreaktion (reduktion, dehydratisering) genomförd i ett enda reaktionskärl.   Med detta projekt har dessa reaktioner för första gången testats på den här typen av molekyler. Det krävs mer optimering eftersom utbytena var låga till medelhöga. Utav sex möjliga substrat fungerade additionsreaktionen med TDAE med fyra stycken. I detta försök testades dock endast en cyklisk reaktion på additionsprodukten. Med ytterligare förbättringar av reaktionsvillkor och upparbetningar förväntas man kunna producera önskad produkt i gott utbyte.