Mechanistic details on the regulation of striated muscle contraction still need to be determined, particularly the specific structural locations of the elements comprising the thick and thin filaments. Of special interest is the location of the regulatory component, troponin, on the actin filament and how its presence influences the behavior of myosin binding to the thin filament. In the present study: (1) Luminescence resonance energy transfer was used to monitor potential conformational changes in the reconstituted thin filament between the C-terminal region of troponin T and myosin subfragment 1; (2) Location of troponin in previously derived atomic models of the acto-myosin complex was mapped to visualize specific contacts; and (3) Shortened tropomyosin was engineered and protein binding and ATPase assays were performed to study the effect of myosin binding close to the troponin complex. Analysis of the results suggest the following: (1) Irrespective of calcium levels, the C-terminal region of troponin T is located close to myosin loop 3 and a few actin helices that may perturb strong acto-myosin interactions responsible for force production. (2) Atomic models indicate myosin subfragment 1 cannot attain the post- powerstroke state due to the full motion of the lever arm being sterically hindered by troponin. (3) A shortened tropomyosin with five actin binding modules (instead of the native seven in muscle cells) binds actin contiguously in a head-to-tail manner and serves to increase the periodicity of troponin complexes on the actin filament. Such behavior eliminates the structure of the actin filament being responsible for the binding location of tropomyosin. (4) Differential behavior of myosin subfragment 1 i.e. (a) binding adjacent to troponin and (b) binding further away from troponin, is apparent as tropomyosin and troponin appear to govern the regions or "target zones" where myosin can bind productively along the actin filament. Physiologically, myosins able to bind close to troponin, but not participate in force production may function as mechanical sensors to attenuate or dampen the force generated from the so-called "target zones". Therefore, this could be a pseudo-regulatory mechanism that functions to protect the contractile apparatus from damage.

An investigation into the relaxation of highly vibrationally excited trifluorobenzene and tetrafluorobenzene following collisions with carbon dioxide was performed using diode laser transient absorption spectroscopy. A 248 nm excimer laser prepared the vibrationally hot (E'~41,000 cm-1) fluorobenzene molecules. Large amounts of translational and rotational energy are transferred through collisions between the hot donor molecule and CO2. Rate constants and collisional probabilities were calculated by probing the high J states (J=58~80) of CO2 in the vibrational ground state, 0000, with measurements taken 1 µsec, ¼ the mean gas collision time, following each excimer laser pulse. The energy transfer probability distribution function, P(E,E'), was calculated for each molecule using the state-resolved probabilities and the energy gain of the bath. The study found a relationship between the fraction of strong collisions and the donor's dipole moment. Additionally, these findings support an application of Fermi's Golden rule to collisional energy transfer by linking the shape of P(E,E') to the shape of the donor's density of states as a function of ΔE.

This thesis consists of two parts and nine chapters. The first part (Part I) presents theoretical studies on non-radiative mode of excitation energy transfer (EET) in donor-acceptor (D-A) systems involving metal nanoparticles. Part I contains four chapters and describes EET in following different D-A systems: (i) dye and a spherical metal nanoparticle of different sizes, (ii) two spherical metal nanoparticles, and (iii) two prolate shaped metal nanoparticles at different relative orientations. Part II provides a detailed study on the origin of photochemical funneling of excitation energy in conjugated polymers like poly-[phenylenevinylene] (PPV) and consists of three chapters. The ninth chapter provides a concluding note. The thesis begins with a basic introduction on Forster resonance energy transfer(FRET), presented in chapter 1. This chapter provides a detail derivation of Forster’s rate expression for a non-radiative process of EET from a donor to an acceptor molecule and discusses the limitations of Forster theory. The chapter highlights the huge success of FRET technique in understanding biological processes assisted by changes in conformations of biopolymers under conditions where Frster theory is valid. The chapter also discusses practical limitations of FRET technique such as use of pre-averaged value of orientation factor and photobleaching of dye molecules. Part I starts with chapter 2 which explains the advantages of using metal nanoparticles over dye molecules in D-A systems. The chapter discusses recent experimental re-ports of excitation energy transfer to nanoparticles, now commonly referred to as nanoparticle surface energy transfer (NSET). Theories describing the process of EET from a dye molecule (dye molecule is assumed to be a point dipole) to a planar metallic surface are discussed. In the case of energy transfer from a donor dye molecule to a planar metallic surface, the distance dependence of the rate of EET is found to vary as 1/d4 where dis a distance from the center of a dye molecule to the metallic surface. This is unlike conven-tional FRET where rate of EET follows 1/R6 distance dependence with R as a distance between the centers of D and A. Also, a recent experimental study by Yun et al [J. Am. Chem. Soc. 127, 3115 (2005)] on energy transfer from a dye molecule to a spherical gold nanoparticle reports that the rate of EET follows 1/d4 distance dependence. The remaining chapters of this part focus on understanding this deviation from the Forster theory in different D-A systems. Chapter 3 describes quantized electro-hydrodynamic approach used to model the plasmonic excitations in metal nanoparticles. The optical absorption frequencies of nanoparticles computed here are subsequently used in chapters 4 and 5 for the calculation of the rate of EET. The chapter discusses the merits and de-merits of electro-hydrodynamic approach in comparison to other available techniques. The electro-hydrodynamic method of calculating the absorption frequencies provide a physically appealing, mathematically simple and numerically tractable approach to the problem and is also at the same time, semi-quantitatively reliable. The optical frequencies obtained as a function of size and aspect ratio of metal nanoparticles are found to be in good agreement with physical predictions. Chapter 4 studies the distance dependence of rate of EET for a D-A system similar to one studied by Yun et al [J. Am. Chem. Soc. 127, 3115 (2005)]. The chapter contains the relevant derivations of the quantities required for computing the interaction matrix elements. The dependence of the rate of EET on R is found surprisingly to be in agreement with Forster theory even at intermediate distances compared to the size of spherical nanoparticles (a). However, the dependence of rate of EET on d is found to vary as 1/dσwith σ=3 - 4 at intermediate distances which is in good agreement with the experimental results of Yun et al. At large values of d, the distance dependence of rate is found to vary as 1/d6 . The chapter discusses the physical basis behind these results. The theory predicts a non-trivial dependence of rate on the size of a nanoparticle which ultimately attains the asymptotic a3 size dependence. The rate of EET is also studied for different orientations of dye molecule. Chapter 5 studies surface plasmon mediated EET between two metal nanoparticles. The rate of EET between two prolate and spherical shaped silver nanoparticles is studied as a function of Rand d. d, in present chapter denotes surface-to-surface separation distance between two nanoparticles. In case of EET between two non-spherical nanoparticles, even at separations larger than the size of the nanoparticle, a significant deviation from 1/R6 dependence is obtained. However, 1/R6 distance dependence of EET rate is found to be robust for spherical nanoparticles over an entire range of separations. The deviation of rate from 1/R6 distance dependence becomes more pronounced with in-crease in the aspect ratio of the nanoparticle. The relative orientation of the nanoparticles is found to markedly influence the R-dependence of EET rate. Interestingly, the relative orientation of nanoparticles effect the d-distance dependence of the rate to a lesser extend in comparison to the R-dependence of the rate. Therefore, we predict that for non-spherical nanoparticles studying EET rate as a function of will provide more conclusive results. The chapter also discusses the size dependence of rate of EET for this particular D-A system. In Part II, excitation energy transfer (EET) in a conjugated polymer is studied. To start with, chapter 6 provides a brief introduction to photophysics of conjugated polymers. The chapter discusses the nature of photoexcitations in these systems and stresses on the influence of polymer’s morphology on the optical properties of conjugated polymers. Chapter 7 describes the theory used for modeling conjugated polymer chain. A polymer chain consists of number of spectroscopic units (chromophores) of varying lengths. The average length of chromophores in conjugated polymer depends on defect concentration. In the present study we treat an excitation generated on each chromophore within “particle-in-a-box” formalism but one that takes into account the electron-hole interactions. The transition dipole moments and the radiative rates are computed for different lengths of chromophores with parameters appropriate for PPV chain. These quantities are used in chapter 8 for calculating the absorption and emission spectra of conjugated polymer chains at different defect concentrations. The main aim of Chapter 8 is to understand the origin of photochemical funneling of excitation energy in conjugated polymers. PPV chain is modeled as a polymer with the length distribution of chromophores given either by a Gaussian or by a Poissonian distribution. We observe that the Poissonian distribution of length segments explains the optical spectra of PPV rather well than the Gaussian distribution. The Pauli’s master equation is employed to describe the excitation energy transfer among different chromophores. The rate of energy transfer is assumed to be given here, as a first approximation, by the well-known Forster expression. The observed excitation population dynamics confirm the photochemical funneling of excitation energy from shorter to longer chromophores of the polymer chain. The calculations show that even in steady state more than one type of chromophore contribute towards the emission spectrum. The observed difference between the calculated emission spectra at equilibrium and in steady state indicates the existence of local domains in a polymer chain within which the non-radiative excitation energy transfer from shorter to longer chromophores take place. These results are found to be in agreement with recent experimental reports. The concluding chapter 9 gives a brief summary of the outcome of the thesis and ends up with suggestion of a few future problems which in current scenario are of great interest.

This research is focused on single-collision energy transfer events between highly vibrationally excited benzene-like donor molecules and small bath molecules, CO2 and N2O in the vibrational ground level. Measuring how much energy is transferred from donors to bath molecules was accomplished by probing bath molecules scattered into specific-rotational states using a tunable Δv=0.0003 cm-1 solid state diode laser. The normalized energy transfer probability distribution function, P(E,E'), determined from energy gain information, is very useful in comparing collisional energy transfer efficiency between various collision systems. P(E,E') is also used to investigate the effects of donor and bath physical properties on collisional energy transfer. The first chapter details the C6H5F–CO2 system, which is the basis of a study on the effect of donor fluorination on strong collision energy transfer. The second chapter is about all fluorobenzene–CO2 systems, which investigates the effect of excess vibrational excitation energy of donors on supercollision energy transfer efficiency as well as donor fluorination effect. The third chapter focuses on how the physical properties of bath molecules affect supercollision energy transfer by measuring state-specific energy gain of N2O scattered into 0000, J=59−75. Instead of CO2, N2O was used as a bath molecule with a pyrazine donor to compare energy gain results of bath molecules with somewhat different physical properties. N2O and CO2 are isoelectronic and have similar mass, but N2O has a small dipole moment. Comparison of P(E,E') obtained from pyrazine–CO2, –N2O, –DCl, and –H2O systems helps to elucidate the effect of the bath physical properties on supercollision energy transfer efficiency. The last chapter is dedicated to the extension of the measurement range of N2O energy gain to the mid J states (J=37–75). In this chapter I discuss reliability of P(E,E') obtained from only high J tail as well as the correction of overall energy transfer rate constant.

Résumé : Le travail de recherche présenté dans ce mémoire fut inspiré par le processus de la photosynthèse qui se produit chez les plantes. Au cours de ce processus l’énergie solaire est convertie en énergie chimique via différentes étapes de transferts d’électrons et d’énergie. En maîtrisant bien ces concepts, de nombreuses applications, telles que les cellules photovoltaïques ou les DEL (Diodes électro-luminescentes) peuvent être améliorées. Pour se faire, il est important d’optimiser les propriétés des matériaux existants (oligomères, polymères, etc…) en préparant des systèmes conjugués plus efficaces, mais aussi de pleinement comprendre les processus qui s’y produisent (processus de transferts d’électrons et d’énergie photo-induist). La série d’oligomères et de polymères présentée dans ce mémoire le sont pour leurs applications dans des systèmes photoniques. Dans cette optique, ce mémoire a été divisé en cinq grands chapitres. Le premier présente les principes théoriques de la photophysique. Le second présente le suivi du transfert d’énergie T[indice inférieur 1] dans les états triplets, T[indice inférieur 1], une dyade constituée de la tétraphénylporphyrine de zinc(II), [ZnTPP], et de la bis(phénylpyridinato)(bipyridine) d’iridium(III), [Ir], chromophores liés avec un pont trans-diéthynylbis(phosphine)-platine(II). Malgré que cette dyade soit entièrement conjuguée et qu’elle soit constituée d’un donneur ([ZnTPP]) et d’un accepteur ([Ir]), aucun transfert d’énergie T[indice inférieur 1] [Ir] → S[indice inférieur 1]/T[indice inférieur 1] [ZnTTP] n’a été observé. Ce résultat fut attribué à l’absence de recouvrement des orbitales moléculaires entre la HSOMO(donneur*) et la HSOMO(accepteur), LSOMO(accepteur) and LSOMO (donneur*) (mécanisme de Dexter). Ainsi, l’échange d’électrons est impossible. Ce chapitre suggère que l’équation de Dexter, k[indice inférieur Dexter] = KJexp(-2r[indice inférieur DA]/L) ne reste qu’une approximation. Ce travail a été publié dans ChemComm (2013, 49, 5544-5546). Le troisième chapitre présente le transfert d’énergie singulet beaucoup lent qu’attendu se produisant dans une dyade constituée d’une porphyrine de zinc(II) avec une porphyrine base libre liées par un pont palladium(II) (trans-PdI[indice inférieur 2]). Sachant que cette dyade est entièrement conjuguée et que la distance entre les deux centres de masse des porphyrines est relativement courte, ce système aurait dû présenter un transfert d’énergie très rapide, d’après la théorie de Förster. Dans ce cas, ce comportement a été expliqué par le faible recouvrement des orbitales frontières (OM) du donneur et de l’accepteur. Ce travail a été accepté le 2014-05-26 dans Chemistry – A European Journal (chem.201403146). Le quatrième chapitre rapporte une étude du transfert d’énergie ultra-rapide (650 fs) entre des états singulets dans une dyade composé d’une porphyrine de zinc(II) (le donneur) et une porphyrine base libre (l’accepteur) liées à l’aide d’un pont de palladium ([beta],[beta]--trans-Pd(NH)[indice inférieur 2](CO)[indice inférieur 2]). Ces résultats ont été attribués à la présence d’un couplage fort entre les OM du donneur et de l’accepteur et de la très faible contribution (atomique) du Pd(II) vers ces OM. Cette dyade montre la plus rapide constante de transfert d’énergie k[indice inférieur ET] que nous connaissons pour des dyades similaires contentant un fragment métallique. Les résultats du troisième et quatrième chapitre montrent que la théorie de Förster tel quel ne suffit pas pour prédire les vitesses de transferts d’énergie dans certains systèmes : d’autres facteurs doivent être pris en compte. Ce travail a été soumis dans JACS ( ja-2014-061774, 19-6-2014). Dans le cinquième chapitre de ce mémoire, la synthèse du bis(-[alpha]-(amino(4-éthynylbenzene (triméthylsilane)(R))))bis(4-éthynylbenzene-(triméthylsilane))quinone diimine (R= H, Boc) comme modèle pour des polymères conjugués et non-conjugués contenant le colorant porphyrine a été proposée. Le corps du composé désiré (tétrakis(4-éthynlyphenyl)quinone-1,4-diimine-2,5-diamine) a montré un transfert de charge partant des groupes terminaux riches en électrons une la benzoquinone centrale plus pauvre. La nature de l’émission fut observée uniquement à 77K pour le cas où R = H et fut attribuée à de la fluorescence. À température ambiante, l’intensité était trop faible pour être observée. Dans le cas où R = Boc, aucune emission n’a été détectée. Malheureusement, le composé espéré ne fut pas obtenu, le procédé de synthèse employé engendra uniquement la forme réduite. Cette forme fut malgré tous analysé, et ne présenta pas de transfert de charge ni de communication entre les différents chromophores. Ceci a été expliqué simplement par le fait que la conjugaison est brisée quand ce composé est sous sa forme réduite. Ce travail sera soumis au Journal of Inorganic and Organometallic Polymers and Materials. // Abstract : The research work presented in this master thesis is inspired by the photosynthetic process occurring in plants where solar energy is converted into chemical energy via several energy and electron transfer processes. In the light of these concepts, several applications such as solar cells and light emitting diodes can be improved. To do so, we need to optimize the properties of polyads, oligomers and polymers to device more efficient conjugated materials as well as developing a full understanding of the photo-induced energy and electron transfer processes that occur. Several organometallic oligomers and polymers are presented in this thesis due to their potential photonic applications. In this respect, this master thesis has five chapters. The first one introduces some theoritical principles of photophysics. The second one presents the monitoring of triplet state (T[subscript 1]) energy transfer in a dyad that consists of zinc(II)tetraphenylporphyrin, [ZnTPP], and bis(phenylpyridinato)-(bipyridine)iridium(III), [Ir], chromophores linked by a platinum(II) containing bridge. Despite the conjugation in this dyad and the presence of the [ZnTPP] energy donor and the [Ir] energy acceptor species, no T[subscript 1] [Ir] → S[subscript 1]/T[subscript 1] [ZnTTP] energy transfer occurs. This result was explained by the absence of MO overlap between HSOMO(donor*) and HSOMO(acceptor), LSOMO(donor*) and LSOMO(acceptor) , and hence no efficient double electron transfer exchange (i.e. Dexter mechanism) is likely to occur. This chapter suggested that Dexter formulation, k[subscript Dexter] = KJexp(-2r[subscript DA]/L), appears as an approximation. This work has been published in ChemComm (2013, 49, 5544-5546). The third chapter shows an unexpected slow singlet energy transfer in a dyad built upon a zinc(II)porphyrin and the corresponding free base chromophores linked by a palladium(II)- containing bridge (trans-PdI[subscript 2]), despite the presence of conjugation and the relative short center-to-center distance. This behavior was explained by two factors, the first is the lack of large molecular orbitals (MOs) overlaps between the frontier MOs of the donor and acceptor, and thus preventing a double electron exchange to occur through the trans-PdI[subscript 2] bridge. The second factor affected the energy transfer is the electronic shielding induced by the presence of this same linker, namely the electron rich iodides, preventing the two VI chromophores to fully interact via their transition dipoles. This work has been accepted on 2014-05-26 in Chemistry-A European Journal (chem.201403146). The fourth chapter reports an ultrafast singlet energy transfer (650 fs) in a dyad composed of a zinc(II)porphyrin (donor) and a free base porphyrin (acceptor) [beta],[beta]-linked via trans- Pd(NH)[subscript2](C=O)[subscript 2]. These results were explained by the presence of strong MO couplings of the donor and acceptor and the very weak atomic contribution of the Pd(II) atom to this MO. This dyad shows the fastest energy transfer rate k[subscript ET] among other similar dyad systems incorporating a bridge either in the form of a metal fragment or carbon-based. The results of these third and fourth chapters showed that the Förster mechanism is not enough to account for the energy transfer in some systems and other factors affect that transfer. This work has been submitted in JACS ( ja-2014-061774, 19-6-2014). In chapter 5, the synthesis of bis-[alpha]-(amino(4-ethynylbenzene (trimethylsilane)(R))bis(4- ethynylbenzene-(trimethylsilane))quinone diimine (R = H, Boc) as a model for conjugated and unconjugated porphyrin dye polymers was proposed. The central core of the desired compound, tetrakis(4-ethynlypenyl)quinone-1,4-diimine-2,5-diamine, provided evidence for a charge transfer interaction from the electron richer terminal groups to be more electron poorer benzoquinone ring. The nature of the emission of the core compound was found to be fluorescence at 77K for the case R = H but was too weak to be observed at 298K. No emission was detected for the case R = Boc. Unfortunately, the synthetic route of the desired compound gave the reduced form. The analyses of the reduced compound showed the complete absence of the charge transfer or any communication between the different chromophores due to the broken conjugation between the porphyrin units in the reduced product. This work will be submitted to Journal of Inorganic and Organometallic Polymers and Materials.

The emerging field of nanotechnology, which spans diverse areas such as nanoelectronics, medicine, chemical and pharmaceutical industries, biotechnology and computation, focuses on the development of devices whose improved performance is based on the utilization of self-assembled nanoscale components exhibiting unique properties owing to their miniaturized dimensions. The first phase in the conception of such multifunctional devices based on integrated technologies requires the study of basic principles behind the functional mechanism of nanoscale components, which could originate from individual nanoobjects or result as a collective behaviour of miniaturized unit structures. The comprehensive studies presented in this thesis encompass the mechanical, dynamical and photophysical aspects of three nanoscale systems. A newly developed europium sulfide nanocrystalline material is introduced. Advances in synthetic methods allowed for shape control of surface-functionalized EuS nanocrystals and the fabrication of multifunctional EuS-CdSe hybrid particles, whose unique structural and optical properties hold promise as useful attributes of integrated materials in developing technologies. A comprehensive study based on a new class of multifunctional nanomaterials, derived from the basic unit of barcoded metal nanorods is presented. Their chemical composition affords them the ability to undergo autonomous motion in the presence of a suitable fuel. The nature of their chemically powered self-propulsion locomotion was investigated, and plausible mechanisms for various motility modes were presented. Furthermore functionalization of striped metallic nanorods has been realized through the incorporation of chemically controlled flexible hinges displaying bendable properties. The structural aspect of the light harvesting machinery of a photosynthetic cryptophyte alga, Rhodomonas CS24, and the mobility of the antenna protein, PE545, in vivo were investigated. Information obtained through a combination of steady-state and time-resolved spectroscopy in conjunction with quantum chemical calculations aided in the elucidation of the dynamics and the mechanism of light harvesting in the multichromophoric phycobiliprotein phycocyanin PC645 in vitro. Investigation of the light-harvesting efficiency and optimization of energy transfer with respect to the structural organization of light-harvesting chromophores on the nanoscale, can provide us with fundamental information necessary for the development of synthetic light-harvesting devices capable of mimicking the efficiency of the natural system.

The main goal of this thesis is to investigate and develop the physics of dye-based photovoltaic physics through molecular and photonic routes. Numerous photovoltaics devices have been fabricated through the course of this work to study their characteristics, performance, physical composition and action. The relative youth of the field of dye-based optoelectronics provides extensive scope for new research which provides fascinating opportunities in terms of physical processes.This thesis is divided into two main projects; exploring the adaption of conventional dye-sensitized solar cells via starkly different routes which serendipitously culminated in striking similarities at their conclusion. The first route is through incorporating spectrally complementary dye molecules with the intention of extending the range of light absorption of the final devices. This initial aim was achieved and was then furthered by the realisation of an unexpected and unprecedented energy transfer process occurring, imparting enhanced photocurrent generation in both the near-IR and visibile region. The second route involves investigating the effect on dye-sensitized solar cell physics and performance of the inclusion of metallic nanoparticles with the expectation of inducing plasmonic interactions. Novel systems were designed and implemented, devices were made which display significant performance enhancement, attributed to plasmonic coupling into the dyes and thereby increasing photocapture. A number of other investigations are documented whose current completion does not sufficiently warrant independent chapters but whose scientific interest is evident.

Résumé : Les transferts d’électrons photo-induits et d’énergie jouent un rôle primordial dans un grand nombre de processus photochimiques et photobiologiques, comme la respiration ou la photosynthèse. Une très grande quantité de systèmes à liaisons covalentes ont été conçus pour copier ces processus de transferts. Cependant, les progrès sont, en grande partie, limités par les difficultés rencontrées dans la synthèse de nouveaux couples de types donneurs-accepteurs. Récemment, des espèces utilisant des liaisons non-covalentes, comme les liaisons hydrogènes, les interactions [pi]-[pi], les liaisons de coordination métal-ligands ou encore les interactions électrostatiques sont le centre d’un nouvel intérêt du fait qu’ils soient plus faciles à synthétiser et à gérer pour obtenir des comportements de transferts d’électrons ou d’énergie plus flexibles et sélectifs. C’est dans cette optique que le travail de cette thèse a été mené, i.e. de concevoir des composés auto-assemblés avec des porphyrines et un cluster de palladium pour l’étude des transferts d’électrons photo-induits et d’énergie. Cette thèse se divise en quatre parties principales. Dans la première section, le chapitre 3, deux colorants porphyriniques, soit le 5-(4-carboxylphényl)-10, 15, 20-tristolyl(porphyrinato)zinc(II) (MCP, avec Na+ comme contre-ion) et 5, 15-bis(4-carboxylphényl)-15, 20-bistolyl(porphyrinato)zinc(II) (DCP, avec Na+ comme contre-ion) ont été utilisés comme donneurs d’électrons, et le [Pd3(dppm)3(CO)]2+ ([Pd32+], dppm = (Ph2P)2CH2, PF6‾ est le contre-ion) a été choisi comme accepteur d’électrons. La structure de l’assemblage [Pd32+]•••porphyrine a été élucidée par l’optimisation des géométries à l’aide de calculs DFT. La spectroscopie d’absorption transitoire (TAS) montre la vitesse de transferts d’électrons la plus rapide (< 85 fs, temps inférieurs à la limite de détection) jamais enregistrée pour ce type de système (porphyrine-accepteur auto-assemblés). Généralement, ces processus sont de l’ordre de l’échelle de la ps-ns. Cette vitesse est comparable aux plus rapides transferts d’électrons rapportés dans le cas de systèmes covalents de type porphyrine-accepteur rapide (< 85 fs, temps inférieurs à la limite de détection). Ce transfert d’électrons ultra-rapide (ket > 1.2 × 1013 s-1) se produit à l’état énergétique S1 des colorants dans une structure liée directement par des interactions ioniques, ce qui indique qu’il n’est pas nécessaire d’avoir de forts liens ou une géométrie courbée entre le donneur et l’accepteur. Dans une deuxième section, au chapitre 4, nous avons étudié en profondeur l’effet de l’utilisation de porphyrines à systèmes π-étendus sur le comportement des transferts d’électrons. Le colorant 9, 18, 27, 36-tétrakis-meso-(4-carboxyphényl)tétrabenzoporphyrinatozinc(II) (TCPBP, avec Na+ comme contre-ion) a été sélectionné comme candidat, et le 5, 10, 15, 20-tétrakis-meso-(4-carboxyphényl)porphyrineatozinc(II) (TCPP, avec Na+ comme contre-ion) a aussi été utilisé à des fins de comparaisons. TCPBP et TCPP ont, tous deux, été utilisés comme donneurs d’électrons pour fabriquer des assemblages supramoléculaires avec le cluster [Pd32+] comme accepteur d’électrons. Les calculs DFT ont été réalisés pour expliquer les structures de ces assemblages. Dans les conditions expérimentales, ces assemblages sont composés principalement d’une porphyrine avec 4 équivalents de clusters. Ces systèmes ont aussi été investigués par des mesures de quenching (perte de luminescence), par électrochimie et par d’autres techniques. Les transferts d’électrons (< 85 fs; temps inférieurs à la limite de détection) étaient aussi observés, de façon similaire aux assemblages MCP•••[Pd32+] et [Pd32+]•••DCP•••[Pd32+]. Les résultats nous indiquent que la modification de la structure de la porphyrine vers la tétrabenzoporphyrine ne semble pas influencer le comportement des cinétiques de transferts d’électrons (aller ou retour). Dans la troisième section, le chapitre 5, nous avons synthétisé la porphyrine hautement [pi]-conjuguée: 9, 18, 27, 36-tétra-(4-carboxyphényléthynyl)tétrabenzoporphyrinatozinc(II) (TCPEBP, avec Na+ comme contre-ion) par des fonctionnalisations en positions meso- et β, β-, qui présente un déplacement vers le rouge de la bande de Soret et des bandes Q. TCPEBP était utilisé comme donneur d’électrons pour fabriquer des motifs supramoléculaires avec le [Pd32+] comme accepteur d’électrons. Des expériences en parallèle ont été menées en utilisant la 5, 10, 15, 20-tétra-(4-carboxyphényl)éthynylporphyrinatozinc(II) (TCPEP, avec Na+ comme contre-ion). Des calculs DFT et TDDFT ont été réalisés pour de nouveau déterminer de façon théorique les structures de ces systèmes. Les constantes d’association pour les assemblages TCPEBP•••[Pd32+]x sont les plus élevées parmi tous les assemblages entre des porphyrines et le cluster de palladium rencontrés dans la littérature. La TAS a montré, encore une fois, des processus de transferts d’électrons dans des échelles de l’ordre de 75-110 fs. Cependant, les transferts de retour d’électrons sont aussi très rapides (< 1 ps), ce qui est un obstacle potentiel pour des applications en cellules solaires à pigment photosensible (DSSCs). Dans la quatrième section, le chapitre 6, les transferts d’énergie triplets (TET) ont été étudiés pour les assemblages MCP•••[Pd32+] et [Pd32+]•••DCP•••[Pd32+]. Les analyses spectrales des états transitoires dans l’échelle de temps de la ns-[mu]s démontrent de façon évidente les TETs; ceux-ci présentent des transferts d’énergie lents et/ou des vitesses moyennes pour des transferts d’énergie T1-T1 (3dye*•••[Pd32+] → dye•••3[Pd32+]*) opérant à travers exclusivement le mécanisme de Förster avec des valeurs de kET autour de ~ 1 × 105 s-1 selon les mesures d’absorption transitoires à 298 K. Des forces motrices non-favorables rendent ces types de processus non-opérants ou très lents dans les états T1. L’état T1 de [Pd32+] (~8190 cm-1) a été qualitativement déterminé par DFT et par la mise en évidence de l’émission S0 ← Tn retardée à 680-700 nm provenant de l’annihilation T1-T1, ce qui fait que ce cluster peut potentiellement agir comme un donneur à partir de ses états Tn, et accepteur à partir de T1 à l’intérieur de ces assemblages. Des pertes d’intensités de types statiques pour la phosphorescence dans le proche-IR sont observées à 785 nm. Ce travail démontre une efficacité modérée des colorants à base de porphyrines pour être impliquée dans des TETs avec des fragments organométalliques, et ce, même attachées grâce à des interactions ioniques. En conclusion, les assemblages ioniques à base de porphyrines et de clusters de palladium présentent des propriétés de transferts d’électrons S1 ultra-rapides, et des transferts d’énergie T1 de vitesses modérées, ce qui est utile pour de possibles applications comme outils optoélectroniques. D’autres études, plus en profondeur, sont présentement en progrès. / Abstract : Photoinduced electron and energy transfers play the pivotal role in various photochemical and photobiological redox processes including photosynthesis and respiration. Abundant covalently bonded systems have been designed to mimic the natural electron and energy transfer processes. However, the progress is often interfered by the difficulties to synthesize novel and versatile covalent donor-acceptor pairs. Recently, entities utilizing non-covalent interactions including hydrogen-bonding, [pi]-[pi] stacking, metal-ligand coordination and electrostatic interactions are becoming a hot topic since they are easy to be fabricated and tuned for selective and flexible electron and energy transfer behaviors. In this respect, the work presented in this thesis designed self-assemblies with porphyrins and a palladium cluster for photoinduced electron and energy transfers. It includes four main sections. In the first section, Chapter 3, two porphyrinic dyes, 5-(4-carboxylphenyl)-10, 15, 20-tristolyl(porphyrinato)zinc(II) (MCP, as sodium salt) and 5, 15-bis(4-carboxylphenyl)-15, 20-bistolyl(porphyrinato)zinc(II) (DCP, as sodium salt), were used as electron donors, and [Pd3(dppm)3(CO)]2+ ([Pd32+], dppm = (Ph2P)2CH2, as PF6‾ salt) cluster was adopted as the electron acceptor. The structure of [Pd32+]•••porphyrin assemblies was elucidated by geometry optimization using Density Functional Theory (DFT) calculations. Transient absorption spectroscopy (TAS) indicated a record fast electron transfer rate (< 85 fs, the time resolution limit) among the porphyrin-acceptor self-assemblies. Typically, these occur in ps-ns time scale. This rate is also comparable to the fastest electron transfer rate reported for the covalently linked porphyrin-acceptor systems (~ 50 fs, the time resolution limit). The ultrafast photo-induced electron transfers (ket > 1.2 × 1013 s-1) occurring at the S1 levels of the dyes in the structurally well-defined “straight up” ionic assemblies indicate that it is not necessary to have a strong bond and bent geometry between the donor and acceptor. In the second section, Chapter 4, we further studied the effect of using π-extended porphyrins on the electron transfer behavior of these assemblies. 9, 18, 27, 36-Tetrakis-meso-(4-carboxyphenyl)tetrabenzoporphyrinatozinc(II) (TCPBP, as a sodium salt) was selected as the candidate, and the 5, 10, 15, 20-tetrakis-meso-(4-carboxyphenyl)porphyrinatozinc(II) (TCPP, as a sodium salt) dye was also studied for comparison purposes. TCPBP and TCPP were both utilized as electron donors to fabricate supramolecular assemblies with the [Pd32+] cluster as the electron acceptor. DFT calculations were used to explain the structure of these assemblies. Under the experimental conditions used, these assemblies mainly exist in the form of one porphyrin with four equivalent clusters. These systems were also investigated by quenching measurements, electrochemistry, and other techniques. Ultrafast electron transfers (< 85 fs; time resolution limit) were also observed, which is similar as those for MCP•••[Pd32+] and [Pd32+]•••DCP•••[Pd32+] assemblies. The results indicate the structural modification from porphyrin to tetrabenzoporphyrin does not seemingly influence the kinetic behavior of the forward and back electron transfers. In the third section, Chapter 5, we synthesized a highly [pi]-conjugated porphyrin, 9, 18, 27, 36-tetra-(4-carboxyphenylethynyl)tetrabenzoporphyrinatozinc(II) (TCPEBP, as a sodium salt) by meso- and β, β-bifunctionalization, which exhibits large red shift of the Soret and Q-bands. TCPEBP was utilized as electron donors to fabricate supramolecular motifs with [Pd32+] cluster as the electron acceptor. Parallel experiments were conducted using 5, 10, 15, 20-tetra-(4-carboxyphenyl)ethynylporphyrinatozinc(II) (TCPEP, as a sodium salt). DFT and TDDFT calculations were applied to elucidate the structure of these assemblies. Binding constants for TCPEBP•••[Pd32+]x is the largest one among all the assemblies with porphyrin and palladium cluster. TAS showed again the ultrafast electron transfer process within the 75-110 fs time frame. However, the back electron transfers are also very fast (< 1 ps), which may be a potential obstacle for future applications in dye-sensitized solar cells (DSSCs). In the fourth section, Chapter 6, triplet energy transfers (TET) of the assemblies MCP•••[Pd32+] and [Pd32+]•••DCP•••[Pd32+] were studied. The transient spectral analysis in the ns-[mu]s time scale clearly demonstrates evidence for TET, which shows a slow to medium T1-T1 energy transfer (3dye*•••[Pd32+] → dye•••3[Pd32+]*) operating through a Förster mechanism exclusively with kET values of ~ 1 × 105 s-1 based on transient absorption measurements at 298 K. Unfavourable reductive and oxidative driving forces make this type of process inoperative or very slow in the T1 states. The T1 state of [Pd32+] (~8190 cm-1) has been quantitatively determined by DFT computations and by evidence for a delayed S0 ← Tn emission at 680-700 nm arising from T1-T1 annihilation, which makes this cluster potentially acting as the energy donor from its Tn state, and T1 acceptor within the assemblies. The static quenching of their near-IR phosphorescence at 785 nm was observed. This work demonstrated a moderate efficiency of the porphyrin dye to be involved in TET with an organometallic fragment, even when attached through ionic interactions. Conclusively, ionic assemblies with porphyrins and palladium clusters exhibit ultrafast S1 electron transfer and moderate T1 energy transfer properties, which is useful for possible application as optoelectronic devices. Further research in more depth is in progress.

Thesis advisor: Abhishek Chatterjee / Förster Resonance Energy Transfer (FRET) offers a powerful approach to study biomolecular dynamics in vitro as well as in vivo. The ability to apply FRET imaging to proteins in living cells provides an excellent tool to monitor important dynamic events such as protein conformational changes, protein-protein interactions, and proteolysis reactions. However, selectively incorporating two distinct fluorophores into the target protein(s) that are capable of FRET interaction within the complex cellular milieu is challenging. Consequently, terminal fusion to genetically encoded fluorescent proteins has emerged as the predominant labeling strategy for FRET studies in vivo. However, a major limitation of this strategy stems from the large size of the fluorescent proteins, which may perturb the native properties of the target, and restricted attachment only to the termini of the target. We reasoned that using genetically encoded fluorescent unnatural amino acids would overcome several of these challenges associated with currently available labeling strategies owing to their small size and the ability to introduce them site- specifically and co-translationally. Here, we report the use of the fluorescent unnatural amino acid “Anap” as a FRET donor with green and yellow fluorescent protein acceptors. We demonstrate the utility of this labeling strategy using proteolysis and conformational change models, and step towards in vivo studies by further developing a proteolysis system in cell lysates. / Thesis (MS) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Devido à necessidade da construção de dispositivos integrados (por exemplo micro laser e inversor óptico), estudos espectroscópicos em amostras altamente dopadas são necessários. Entretanto, o procedimento de se utilizar amostras com alta concentração traz consigo o problema da supressão da luminescência, devido a processos de transferência de energia mais intensos. Portanto, neste trabalho, estudamos os processos de transferência de energia que diminuem a luminescência na região do infravermelho utilizando amostras vítreas à base de fluoreto (fluoroindato e fluorozircoaluminato), dopados com Er+3 em concentrações que variam de 0.1 a 20 mol%Er. Obtivemos parâmetros de transferência de energia através de um modelo para os níveis do Er+3 (sistema de equações diferenciais), microparâmetros de transferência de energia e probabilidades de decaimento radiativo, entre outros. Identificamos dois mecanismos de depolução da região do infravermelho, a migração de energia e a conversão ascendente, e dois mecanismos de população dos níveis 4S3/2 e 4F9/2, a absorção do estado excitado e a conversão ascendente por transferência de energia. A análise dos resultados indicou que a conversão ascendente por transferência de energia é o principal mecanismo de população dos níveis 4S3/2 e 4F9/2 / Given the need of integrated devices, as microchip laser and optical inverter, for instance, spectroscopic studies on samples with large ion doping concentrations are necessary. However, the use of highly doped samples brings with it the problem of luminescence quenching due to intense energy transfer processes. Therefore, in the present work we studied the energy transfer processes that diminish the infrared luminescence in two fluoride glass compositions (fluoroindate and fluorozircoaluminate) doped with Er+3 in the range of 0.1 to 20% molar. For that, we obtained energy transfer parameters using rate equations formalism for Er+3 energy levels. We also obtained the microscopic parameters of energy transfer, and radiative decay rates, among others. Two mechanisms of depopulation of level 4I11/2 were identified, energy migration and up conversion. Similarly the mechanisms responsible for the population of levels 4S3/2 and 4F9/2, were identified as excited state absorption and energy transfer up conversion. The results analysis indicates that the energy transfer up conversion is the major mechanism for the population of levels 4S3/2 and 4F9/2.