The thesis is divided into two major parts. The first part focuses on the localisation of probes in lipid/polymeric bilayers and in GM1 micelles. Included in this thesis is a new approach based on electronic energy transfer/migration (FRET/DDEM), which efficiently determines transversal positions of fluorescent molecules in lipid bilayers. This approach has been used to locate newly synthesized lipid probes in DOPC bilayers. The label was introduced at the end of sn-2 acyl chains of variable length. Analytical models accounting for FRET exist for a limited number of basic geometries. Here, a combination of FRET and Monte Carlo simulations enables the localisation of probes in bicelles and in bilayers containing pores, i.e. in lipid systems with variable curvature, or in non-homogenous lipid systems. This approach has been used to test whether conical-like fluorescence probes have an increased affinity to highly curved regions, which would enable preferential labelling of membrane pores. A simplified FRET model has been applied to localize 2-pyridones, a class of potential drugs, in GM1 micelles. Since the localisation of drugs within nanoparticles might influence the release kinetics and loading efficiency, knowledge about the drug location is highly relevant. It turned out that all derivatives were localised at the core-shell interface of GM1 micelles. The second part of the thesis focuses mainly on the estimation of lipid nanodomain size by means of FRET, which still remains the most powerful method in this field. Limitations of FRET in the determination of domain size have been explored. We showed that the limitations of FRET are mainly caused by a low probes affinity to either the liquid-ordered or liquid-disordered phase. In the continuing work we provided a detailed dynamic and structural study of crosslinker-triggered formation of nanodomains. Here, two different domains have been revealed, i.e. i) domains whose size grows with increasing amount of added cholera toxin (CTxB), and to which CTxB binds tightly; ii) domains formed in membranes containing a slightly increased amount of sphingomyelin (as compared to i) whose size does not change during titration by additional CTxB and to which CTxB binds less tightly. / Disertace je rozdělena do dvou hlavníchčástí. Prvníčást se zabývá lokalizací značek v lipidových/polymerních dvojvrstvách a v GM1micelách. V práci prezentujeme nový přístup založený na přenosu/migraci elektronické energie (FRET/DDEM), jež umožňuje efektivně určovat vertikální pozici fluorescenčních molekul uvnitř lipidové dvojvrstvy. Tato metoda byla použita k lokalizaci nově syntetizovaných lipidových značek značených na konci sn-2 acylového řetězce s různou délkou v DOPC dvojvrstvách. Analytické modely popisující FRET existují pouze pro limitovaný počet základních geometrií. Kombinace FRETu s Monte Carlo simulacemi nicméně umožňuje lokalizaci značek v bicelách a v dvojvrstvách obsahujících póry, tj. v lipidových systémech s proměnlivým zakřivením a v nehomogenních lipidových útvarech. Tento přístup umožnil např. zjistit, zda kuželovitětvarované značky mají zvýšenou afinitu k vysoce zakřiveným oblastem dvojvrstvy, což by umožnilo preferenční značení pórů. Lokalizovány byly rovněž tři deriváty 2-pyridonů(potencionálních léčiv) v GM1micelách za použití jednoduchého modelu zohledňujícího FRET mezi donory a akceptory nacházejícími se v micelách. Lokalizace léčiv v nanočásticích ovlivňuje kinetiku uvolňování (release kinetics) a množství látky solubilizované v micelách (loading efficiency). Druhá část se především zabývá určováním velikostí lipidových nanodomén pomocí FRETu, který stále zůstává nejvíce výkonnou metodou v této oblasti. Zkoumány byly limitace FRETu v určování lipidových nanodomén. Ukázalo se, že tato omezení jsou především způsobena nízkou afinitou značek buď k Lonebo k Ldfázi. V navazující studii jsme poskytnuli detailní dynamickou a strukturní studii formace nanodomén indukované crosslinkerem. Objevili jsme dva typy domén: a) domény, jejichž velikost se zvětšuje s rostoucím množstvím přidaného cholera toxinu (CTxB) a k nimž se CTxB váže pevně a b) domény vzniklé v membránách se zvýšeným množstvím sfingomyelinu (ve srovnání s a)), jejichž velikost se nemění během titrace dodatečným CTxB a k nimž se CTxB váže méně pevně. / This thesis has been elaborated within the framework of the Agreement on JointSupervision (co-tutelle) of an International Doctoral Degree Programmebetween Charles University in Prague, Czech Republic and the Department of Chemistry at Umeå University, Sweden.

The studies presented in this thesis explore electronic energy transfer (EET) in light-harvesting antenna complexes and investigate the role of quantum coherence in EET. The dynamics of energy transfer are investigated in three distinct length scales and a different formulation of the exciton transport problem is applied at each scale. These scales include: the scale of a molecular dimer, the scale of a single protein and the scale of a molecular aggregate. The antenna protein phycoerythrin 545 (PE545) isolated from the photosynthetic cryptophyte algae Rhodomonas CS4 is specifically studied in two chapters of this thesis. It is found that formation of small aggregates delocalizes the excitation across chromophores of adjacent proteins, and that this delocalization has a dramatic effect in enhancing the rate of energy transfer between pigments. Furthermore, we investigate EET from a donor to an acceptor via an intermediate site and observe that interference of coherent pathways gives a finite correction to the transfer rate that is sensitively dependent on the nature of the vibrational interactions in the system. The statistical fluctuations of a system exhibiting EET are investigated in the final chapter. The techniques of non-equilibrium statistical mechanics are applied to investigate the steady-state of a typical system exhibiting EET that is perturbed out of equilibrium due to its interaction with a fluctuating bath.

The studies presented in this thesis explore electronic energy transfer (EET) in light-harvesting antenna complexes and investigate the role of quantum coherence in EET. The dynamics of energy transfer are investigated in three distinct length scales and a different formulation of the exciton transport problem is applied at each scale. These scales include: the scale of a molecular dimer, the scale of a single protein and the scale of a molecular aggregate. The antenna protein phycoerythrin 545 (PE545) isolated from the photosynthetic cryptophyte algae Rhodomonas CS4 is specifically studied in two chapters of this thesis. It is found that formation of small aggregates delocalizes the excitation across chromophores of adjacent proteins, and that this delocalization has a dramatic effect in enhancing the rate of energy transfer between pigments. Furthermore, we investigate EET from a donor to an acceptor via an intermediate site and observe that interference of coherent pathways gives a finite correction to the transfer rate that is sensitively dependent on the nature of the vibrational interactions in the system. The statistical fluctuations of a system exhibiting EET are investigated in the final chapter. The techniques of non-equilibrium statistical mechanics are applied to investigate the steady-state of a typical system exhibiting EET that is perturbed out of equilibrium due to its interaction with a fluctuating bath.

Molecular photoabsorption enhancement under ambient solar radiations can improve efficiency substantially in renewable energy production. Here, we explore the theoretical basis and experimental evidences that nanostructured molecular assemblies exhibit an unprecedented property of synergistic photon absorption enhancement. The molecular mechanism of this enhancement phenomenon originates from the combined effect of the photon-molecule interaction and the electronic energy transfer between two adjacent molecular assemblies. For a natural system, the synergistic photon absorption enhancement factor of green algae (Chlorella vulgaris) in vivo at 632.8 nm was determined to be 103. This enhanced photon absorption process in nanostructured molecular assemblies opens a doorway to create entangled double excitons by incoherent solar radiations.

Fluorescence-based techniques are widely used in bioscience, offering a high sensitivity and versatility. In this work, fluorescence electronic energy migration/ transfer is applied to measure intramolecular distances in two types of systems and under various conditions. The main part of the thesis utilizes the process of donor-acceptor energy transfer to probe distances within the ribosomal protein S16. Proteins are essential to all organisms. Therefore, it is of great interest to study protein structure and function in order to understand and prevent protein malfunction. Moreover, it is also important to try to study the proteins in an environment which resembles its natural habitat. Here two protein homologs were investigated; S16Thermo and S16Meso, isolated from a hyperthemophilic bacterium and a mesophilic bacterium, respectively. It was concluded that the chemically induced unfolded state ensemble of S16Thermo is more compact than the corresponding ensemble of S16Meso. This unfolded state compaction may be one reason for the increased thermal stability of S16Thermo as compared to S16Meso. The unfolded state of S16 was also studied under highly crowded conditions, mimicking the environment found in cells. It appears that a high degree of crowding, induced by 200 mg/mL dextran 20, forces the unfolded state ensemble of S16Thermo to become even more compact. Further, intramolecular distances in the folded state of five S16 mutants were investigated upon increasing amounts of dextran 20. We found that the probed distances in S16Thermo are unaffected by increasing degree of crowding. However, S16Meso shows decreasing intramolecular distances for all three studied variants, up to 100 mg/mL dextran. At higher concentrations, the change in distance becomes anisotropic. This suggests that marginally stable proteins like s16Meso may respond to macromolecular crowding by fine-tuning its structure. More stable proteins like S16Thermo however, show no structural change upon increasing degree of crowding. We also investigated the possibility of local specific interactions between the protein and crowding agent, by means of fluorescence quenching experiments. Upon increasing amounts of a tyrosine labelled dextran, a diverse pattern of fluorescence quantum yield and lifetime suggests that specific, local protein-crowder interactions may occur. In a second studied system, electronic energy migration between two donor-groups, separated by a rigid steroid, was studied by two-photon excitation depolarization experiments. Data were analysed by using recent advances, based on the extended Förster theory, which yield a reasonable value of the distance between the two interacting donor-groups. To the best of our knowledge, this is the first quantitative analysis of energy migration data, obtained from two-photon excited fluorescence.

Two chlorophylls of the FMO complex, the light-harvesting complex of the green sulfur bacteria, are modeled as two coupled qubits, each surrounded by one spin-bath simulating the environment. The dynamics of the system at a non-zero temperature provide exact analytical expressions for the transition probability and the coherence. It is shown that the decoherence-inducing interaction with the environment enhances the electronic energy transfer. Also the correlations in terms of entanglement and nonlocality are quantitatively studied, sensitively differing when introducing a decay term to resemble both chlorophylls being in their ground states. It is proved that nonlocality is a stronger form of correlation than entanglement.

L'objectif de cette thèse est la mise en place et l'étude d'un transfert d'énergie électronique réversible (REET), à la suite d’une excitation lumineuse, entre des sous-composants moléculaires au sein d’architectures nanométriques de type rotaxane. Dans un système bichromophorique, lorsque les états excités du chromophore les plus bas sont quasi-isoénergétiques et que la cinétique du transfert interchromophore est rapide, le REET peut être instillé en modifiant les propriétés de l'état excité. Des dérivés du pyrène et du tris(bipyridine)ruthénium(II) ont été choisis comme chromophores appariés. La formation de rotaxane a été catalysée par du cuivre (réactions de Huisgen et Cadiot-Chodkiewicz) au sein d’un macrocycle doté de pyrène, couplant des demi-fils moléculaires comprenant des groupements terminaux volumineux - dont Ru(bpy)32+. Des durées de vie de luminescence prolongée (jusqu'à 14 μs), comparées au parent Ru(bpy)32+, indiquent que des processus de transfert d'énergie électroniques réversibles ont été établis dans une série de rotaxanes de structure variable, sont étudiés par spectroscopies stationnaire et résolue dans le temps. / The focus of this thesis is the establishment and study of reversible electronic energy transfer (REET), following light excitation, between molecular subcomponents within ring-on-thread rotaxane nanometric architectures. When the lowest-lying chromophore excited states are quasi-isoenergetic and kinetics of interchromophore transfer are rapid, REET can be instilled - changing excited-state properties. Pyrene and ruthenium(II) tris(bipyridine) derivatives were chosen as matched chromophores. Rotaxane formation was based on active template copper catalysis (Huisgen and Cadiot-Chodkiewicz reactions) within a pyrene-decorated macrocycle, coupling half threads comprising bulky stopper groups - one of which being Ru(bpy)32+. Prolonged luminescence lifetimes (up to 14 μs), compared to parent Ru(bpy)32+, indicated that reversible electronic energy transfer processes were instilled in a series of rotaxanes of varying structure, which were studied by state-state and time-resolved spectroscopies.

A new and general procedure is described for a detailed analysis of time-resolved fluorescence depolarisation data in the presence of electronic energy migration. An isotropic ensemble of bifluorophoric molecules (D1-R-D2) has been studied to demonstrate its utility. Intramolecular donor-donor energy migration occurs between the two donor groups (D), which are covalently connected to a rigid linker group (R). These groups undergo restricted reorientational motions with respect to the R group. The analysis of depolarisation data basically involves the search for best-fit parameters which describe the local reorienting motions, the interfluorophore D1-D2 distance, as well as the mutual orientations of the donors. For this, the analysis is partly performed in the Fourier domain and the best-fit parameters are determined by using an approach based on a Genetic Algorithm. The energy migration process has been described by using Monte Carlo simulations and an extended Förster theory. It is found that this theory provides the least time-consuming computational method. Since one-photon and two-photon excited fluorescence experiments can be applied for energy migration studies, a general and unified theoretical formulation is given. To exemplify the developed quantitative approach the depolarisation of the fluorescence in the presence of electronic energy migration within a bis-(9-anthrylmethylphosphonate) bisteroid molecule has been studied by time-resolved two-photon excited fluorescence depolarisation experiments. To solely obtain information about local reorientations of the 9-anthrylmethyl group, also the mono-(9-anthrylmethylphosphonate) bisteroid was studied, which enabled modelling of the ordering potential of the donor. Values of the two-photon absorption tensor components were obtained. To describe the discrepancy between the measured values of the initial anisotropy and fundamental anisotropy predicted by theory the distribution of absorption tensor caused by fast processes have been introduced. An angular parameter of absorption tensor was determined. Reasonable values of the distance between the 9-anthrylmethyl groups, as well as for their mutual orientation were obtained.

No description available.

Electronic energy transfer has been investigated in pure donor systems by means of computer simulations. Calculated properties were the probability that the initially excited donor is excited at a time t after the excitation, Gs(t), the mean square displacement of the excitation and different fluorescence observables. For three dimensional systems the results obtained by Monte Carlo simulations were compared to the so-called GAF-theory {Gouchanour,C. R., Andersen, H. C. and Fayer, M. D., J. Chem. Phys. 81, 4380 (1984)}, and the agreement was found to be good. Anisotropic systems, i.e. mono-, bi- and multilayer systems, were compared to the two-particle model {Baumann,J. and Fayer, M. D., J. Chem. Phys. 85, 4087 (1986)}. The agreement between the Gs(t) calculated from the tp- model and the Monte Carlo simulations were good for all systems investigated. However, the agreement between the fluorescence observables obtained by MC and the tp-model were in general poor. A much better agreement was found when a phenomenological approach was used for calculating the fluorescence depolarization ratios. Three dimensional systems where the donors are rotating on the same time scale as the energy transfer takes place have also been studied and compared to analytical theories. The Molecular Dynamics simulations of decapeptide H142 shows that simulations in a continuum with a relative permeability do not provide a reliable alternative to simulations with explicit solvent molecules. / <p>Diss. (sammanfattning) Umeå : Umeå universitet, 1991, härtill 5 uppsatser</p> / digitalisering@umu