How an enzyme achieves such high rates of catalysis in comparison to its solution counterpart reaction has baffled scientists for many decades. Much of our understanding of enzyme function is derived from research devoted to enzyme chemical reactions and analysis of static three-dimensional images of individual enzyme molecules. However, more recently, a role of protein dynamics in facilitating enzyme catalysis has emerged. It is often challenging to probe how protein motions are correlated to and impact on the catalytic cycle of enzymes. Nevertheless, this subject must be addressed to further our understanding of the roots of enzyme catalysis. Herein, this research question is approached by studying the link between protein domain dynamics and electron transfer chemistry in the diflavin oxidoreductase family of enzymes. Previous studies conducted on the diflavin oxidoreductases have implied a role of protein domain dynamics in catalysing electron transfer chemistry. However, diflavin oxidoreductase motions have not been experimentally correlated with mechanistic steps in the reaction cycle. To address these shortcomings, a 'real-time' analysis of diflavin oxidoreductase domain dynamics that occur during enzyme catalysis was undertaken. The methodology involved specific labelling of diflavin oxidoreductases (cytochrome P450 reductase, CPR, and neuronal nitric oxide synthase, nNOS) with external donor-acceptor fluorophores that were further used for time-resolved stopped-flow Förster resonance energy transfer (FRET) spectroscopy measurements. This approach to study enzyme dynamics was further linked with traditional UV-visible stopped-flow approaches that probed enzymatic electron transfer chemistry. Results showed a tight coupling between the kinetics of electron transfer chemistry and domain dynamics in the two diflavin oxidoreductase systems studied. Moreover, through the use of a flavin analogue (5-deazaflavin mononucleotide) and isotopically labelled nicotinamide coenzymes (pro-S/R NADP2H), key steps in the reaction mechanism were correlated with dynamic events in calmodulin, the partner protein of nNOS.The approaches developed in this project should find wider application in related studies of complex electron-transfer enzymes. Altogether, this research emphasises the key link between protein domain motions and electron transfer chemistry and provides a framework to describe the relationship between domain dynamics and diflavin oxidoreductase function.

Made available in DSpace on 2014-06-11T19:30:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-03-31Bitstream added on 2014-06-13T18:41:07Z : No. of bitstreams: 1 paula_lc_dr_sjrp.pdf: 2712667 bytes, checksum: 532220ccc7e56ac66281c7460f0834da (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Neste trabalho é investigada a influência de ambientes complexos na dinâmica de reações de transferência de elétrons. O principal objetivo é demonstrar a ocorrência de fenômenos de intermitência em processos de transferência de elétrons. Entender como estes fenômenos são governados pela ação do solvente e caracterizar a dependência da temperatura, também são parte do propósito deste trabalho. O ambiente polar, no qual ocorre a reação, é tratado de modo simples, seguindo o modelo de Onuchic-Wolynes, e é representado por uma única camada de dipolos em torno da cavidade de carga. O método utilizado para realizar este estudo é através de simulação computacional de Monte Carlo. A dinâmica de solvente é estudada observando-se as razões entre os momentos dos tempos de primeira passagem (first passage time) dos eventos de transferência de elétrons, definido como Rn. Primeiramente é feita uma análise do modelo teórico em que o sistema é caracterizado analiticamente através de parâmetros termodinâmicos. Posteriormente os resultados computacionais são analisados e mostram concordância com a teoria. O sistema apresenta três regiões de temperatura, nas quais, o comportamento cinético da reação se alterna em exponencial, não exponencial e novamente exponencial. / In this work, we have investigated the influence of complex environments on electron transfer reaction dynamics. The main objective in this work is to show the occurrence of intermittence phenomenon on electron transfer reactions. The understanding on how these phenomenons are governed by solvent and the temperature dependence characterization, are also addressed. The polar environment, in which the reaction takes place, is treated in a simple way, following the Onuchic-Wolynes model, and it is represented by a single shell of dipoles around a charge cavity. This study is performed using Monte Carlo simulation method. The solvent dynamic is studied by the observation of the ratios of the first passage time of electron transfer events, defined as Rn. Firstly, it is performed the analysis of the theoretical model in which the system is characterized, analytically, by thermodynamics parameters. Next the computational results are analyzed and it shows agreement with the theory. The system exhibits three temperature regimes, in which, the kinetic behavior of the reaction is changed from exponential, to nonexponential and again to exponential.

Magnetic field effects (MFE) on electrochemical systems have been of interest to researchers for the past 60 years. MFEs on mass transport, such as magnetohydrodynamics and magnetic field gradients effects are reported, but MFEs on electron transfer kinetics have been rarely investigated. Magnetic modification of electrodes enhances electron transfer kinetics under conditions of high concentrations and low physical diffusion conditions, as shown by Leddy and coworkers. Magnetic microparticles embedded in an ion exchange polymer (e.g., Nafion) applied to electrode surfaces. Rates of electron transfer reactions to diffusing redox probes and to adsorbates are markedly enhanced. This work reports MFEs on hydrogen evolution on illuminated p-Si; MFEs on hydrogen evolution on noncatalytic electrodes; a model for MFEs on homogeneous self-exchange reactions; and a convolution based voltammetric method for film modified electrodes. First, a MFE on the photoelectrochemical hydrogen evolution reaction (HER) at p-Si semiconductors is demonstrated. The HER is an adsorbate reaction. Magnetic modification reduces the energetic cost of the HER by 400 - 500 mV as compared to Nafion modified electrodes and by 1200 mV as compared to unmodified p-Si. Magnetically modified p-Si achieves 6.2 % energy conversion efficiency. Second, from HER on noncatalytic electrodes, the MFE on photoelectrochemical cells arises from improved heterogeneous electron transfer kinetics. On glassy carbon electrodes, magnetic modification improves heterogeneous electron transfer rate constant, k₀,for HER 80,000 fold. Third, self exchange reaction rates are investigated under magnetic modification for various temperatures, outersphere redox probes, and magnetic particles. Arrhenius analyses of the rate constants collected from the experiments show a 30 - 40 % decrease in activation energy at magnetically modified electrodes. A kinetic model is established based on transition state theory. The model includes pre-polarization and electron nuclear spin polarization steps and characterizes a majority of the experimental results. Lastly, a convolution technique for modified with uniform films electrodes is developed and coded in Matlab (mathematical software) for simple and straightforward analysis of Nafion modified electrodes.

A growing number of flavoprotein systems have been observed to bifurcate pairs of electrons. Flavin-based electron bifurcation (FBEB) results in products with greater reducing power than that of the reactants with less reducing power. Highly reducing electrons at low reduction midpoint potential are required for life processes of both aerobic and anaerobic metabolic processes. For electron bifurcation to function, the semiquinone (SQ) redox intermediate needs to be destabilized in the protein to suppress its ability to trap electrons. This dissertation examines SQ suppression across a number of flavin systems for the purpose of better understanding the nature of SQ suppression within FBEB and elucidates potential mechanistic roles of SQ. The major achievement of this work is advancing the understanding of SQ suppression and its utility in flavoproteins with the capacity to bifurcate pairs of electrons. Much of these achievements are highlighted in Chapter 6. To contextualize these mechanistic studies, we examined the kinetic and thermodynamic properties of non-bifurcating flavoproteins (Chapters 2 and 3) as well as bifurcating flavoproteins (Chapters 4 and 5). Proteins were selected as models for SQ suppression with the aim of elucidating the role of an intermediate SQ in bifurcation. The chemical reactions of flavins and those mediated by flavoproteins play critical roles in the bioenergetics of all lifeforms, both aerobic and anaerobic. We highlight our findings in the context of electron bifurcation, the recently discovered third form of biological energy conservation. Bifurcating NADH-dependent ferredoxin-NADP+ oxidoreductase I (Nfn) and the non-bifurcating flavoproteins nitroreductase, NADH oxidase, and flavodoxin were studied by transient absorption spectroscopy to compare electron transfer rates and mechanisms in the picosecond range. Different mechanisms were found to dominate SQ decay in the different proteins, producing lifetimes ranging over 3 orders of magnitude. The presence of a short-lived SQ alone was found to be insufficient to infer bifurcating activity. We established a model wherein the short SQ lifetime in Nfn results from efficient electron propagation. Such mechanisms of SQ decay may be a general feature of redox active site ensembles able to carry out bifurcation. We also investigated the proposed bifurcating electron transfer flavoprotein (Etf) from Pyrobaculum aerophilum (Pae), a hyperthermophilic archaeon. Unlike other Etfs, we observed a stable and strong charge transfer band (λmax= 724 nm) for Pae’s Etf upon reduction by NADH. Using a series of reductive titrations to probe bounds for the reduction midpoint potential of the two flavins, we argue that the heterodimer alone could participate in a bifurcation mechanism.

acase@tulane.edu

The association between natural organic matter (NOM) and iron (Fe) minerals was widely found in soil and sediments and has been shown to impact the fate of Fe minerals and NOM. Ferrihydrite, a ubiquitous Fe mineral, serves as important sink for NOM and rapidly transforms to secondary Fe minerals in the presence of Fe(II). The associated NOM has been found to influence the Fe(II)-catalyzed ferrihydrite transformation pathway, but it remains unclear how various NOM affects this transformation and the implication. This study specifically investigates how different species of NOM affect Fe(II)-catalyzed ferrihydrite transformation under different C/Fe ratios. A series of Fe isotope tracer experiments were conducted to measure Fe atom exchange and electron transfer between aqueous Fe(II) and ferrihydrite in the presence of diverse NOM species. The fate of Ni during Fe(II)-catalyzed transformation of NOM-Fh coprecipitate was also investigated. Ferrihydrite was found less susceptible to Fe(II)-catalyzed transformation with increasing C/Fe ratio and fulvic acids and Suwannee River NOM (SRNOM) in the coprecipitates need lower C/Fe ratio than humic acids to completely inhibit formation of secondary Fe minerals. At C/Fe ratios where ferrihydrite transformed to secondary minerals, goethite was dominant in ferrihydrite coprecipitated with humic acids, whereas lepidocrocite was favored in ferrihydrite coprecipitated with fulvic acids and SRNOM. Adsorbed SRNOM may be more inhibitive than coprecipitated SRNOM on Fe(II)-catalyzed ferrihydrite transformation under similar C/Fe ratios. Despite no secondary mineral transformation at high C/Fe ratios, Mössbauer spectra indicated electron transfer still occurred between Fe(II) and ferrihydrite coprecipitated with fulvic acid and SRNOM. In addition, isotope tracer experiments revealed that a significant fraction of structural Fe(III) in the ferrihydrite mixed with the aqueous phase Fe(II) (~85%). After reaction with Fe(II), Mössbauer spectroscopy indicated some subtle changes in the crystallinity, particle size or particle interactions in the coprecipitate. The effect of coprecipitated SRNOM on Ni(II) distribution during Fe(II)-catalyzed ferrihydrite transformation was investigated with adsorbed Ni(II) and coprecipitated Ni(II). Ni(II) adsorbed on ferrihydrite was more resistant to acid extraction after Fe(II)-catalyzed transformation and suggested that structural incorporation of Ni into secondary Fe minerals occurred. With coprecipitated SRNOM, ferrihydrite did not transform to secondary minerals in the presence of Fe(II) but extensive Fe atom exchange between aqueous Fe(II) and structural Fe(III) still occurred. Limited change in Ni stability was observed, suggesting there was only small portion of Ni redistributed in the presence of Fe(II). Pre-incorporated Ni(II) in Ni-SRNOM-Fh coprecipitate was partially released (6-8 %) in the presence of Fe(II), but the distribution of remaining Ni(II) in the solid did not change measurably. Our observation suggests that the presence of SRNOM limited the redistribution of Ni most likely because of limited transformation of ferrihydrite to secondary minerals.

Reactions of aqueous Fe(II) with Fe and Mn oxides influence heavy metal mobility, transformation of trace organics, and important elemental cycles as Fe precipitates form or dissolve, and as electrons move between aqueous and solid phases. Our objective was to characterize reactions of Fe(II) with important metal oxides, using a suite of complementary tools to investigate the extent and underlying mechanisms of Fe(II)-metal oxide redox activity. Nanoscale materials (1-100 nm) may have fundamentally different surface or electronic properties than larger solids. Goethite was synthesized with primary particle dimensions above or below the nanoscale. Despite large differences in particle surface area, goethite nanorods and microrods had similar net Fe(II) sorption and electron transfer properties. Experimental evidence suggested particle aggregation resulted in particle complexes of a similar size, meaning considerations of available reactive surface area could explain our results. Kinetics and extent of Fe(II)-Fe(III) redox reactions between aqueous Fe(II) and goethite were examined using a stable isotope tracer approach. Aqueous Fe(II) that had been enriched in 57Fe was mixed with isotopically-normal goethite. Convergence of Fe isotope ratios in aqueous and solid phases to values predicted by complete Fe atom exchange provided evidence that all goethite Fe(III) atoms could eventually react with Fe(II), despite no evidence for complete atom exchange from bulk measurements of the aqueous or solid phase. Fe isotope data at different experimental conditions was combined with theoretical considerations governing electron transfer in goethite to provide evidence for redox-driven atom exchange involving bulk conduction of electrons between spatially distinct Fe(II) sorption and release sites. Procedures for stable Fe isotope tracer studies have been adapted to investigate redox transformations of magnetite solids with different divalent cation content. Evolution of aqueous Fe(II)-Mn(IV) redox reactions was examined using complementary techniques. After pyrolusite particles were exposed to aqueous Fe(II), aqueous Fe and Mn were analyzed, and X-ray diffraction was utilized with electron microscopy to assess solid phase evolution during continued exposure to Fe(II). Selective use of Fe isotopes during Fe(II) resuspensions allowed us to track chemical changes occurring to one particular Fe addition using 57Fe Mössbauer spectroscopy.

[Formulae and special characters can only be approximated here. Please see the pdf version of the Abstract for an accurate reproduction.] The kinetics for outer-sphere electron transfer between a series of cobalt(II) poly-aza cage ligand complexes and the iron(III) sarcophagine-type hexa-aza cage complex, [Fe(sar)]3+ (sar = 3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane), in aqueous solution have been investigated and the Marcus correlation is used to deduce the electron self-exchange rate constant for the [Fe(sar)]3+/2+ couple from these cross-reactions. The deduced electron self-exchange rate constant is in relatively good agreement with the experimentally determined rate constant (k ex calc = 4 ´ 10 5 M -1 s -1 ; k ex obs = 8 ´ 10 5 M -1 s -1 ). The successful application of the Marcus correlation to the electron transfer reactions of the Fe cage complex is consistent with the trend for the Co, Mn, Ni and Ru cage complexes which all follow the pattern of outer-sphere electron transfer reactivity expected from the Marcus-Hush formalism. A comparison of predictions based on the Marcus correlation with the experimentally determined kinetics of an extended series of cross reactions involving cobalt cage complexes with low-spin-high-spin cobalt(III)/(II) couples shows that electron transfer reactions involving large spin changes at the metal centre are not necessarily anomalous in the context of the adiabatic Marcus-Hush formalism. The results of this study also show that for suitable systems, the Marcus correlation can be used to reliably calculate the rates of outer-sphere electron transfer cross-reactions, with reaction free-energy changes spanning the range -6 to -41 kJ mol -1 and many different combinations of initial electronic configurations. Together, these results provide a coherent and internally consistent set of experimental data in support of the Marcus-Hush formalism for outer-sphere electron transfer. The results with the caged metal-ion systems also highlight the special nature of the mechanism of electron transfer in reactions of metal-aqua ions. ¶ A new range of symmetrically disubstituted hexa-aza sarcophagine-type cage ligand complexes are prepared in this study by the base-catalysed co-condensation of formaldehyde and a-methylene aliphatic aldehydes with cobalt(III) tris(1,2-diamine) precursors in acetonitrile solution. Encapsulation reactions based on the condensation of the weak carbon di-acids propanal and decanal with formaldehyde and the cobalt(III) tris(1,2-diamine) precursors, [Co(en)3 ] 3+ (en = 1,2-ethanediamine) and D-lel3 -[Co((R, R)-chxn)3 ] 3+ (chxn = 1,2-cyclohexanediamine), yield unsaturated cobalt(III) cage complexes with an endo-cyclic imine function in each cap. The Co III -coordinated endo-cyclic imine units of the cage ligands are reactive electrophiles that are readily reduced by the BH4 - ion to give the corresponding symmetrically di-substituted hexaamine macrobicyclic cage ligands. The nitromethane carbanion is also shown to add at the endo-cyclic imine function to yield a novel nitromethylated cage ligand complex. The latter reaction introduces a new method for the regioselective functionalisation of cage ligands at sites removed from the more commonly substituted bridgehead positions. The capping of cobalt(III) tris(1,2-diamine)-type complexes with weak CH-acids developed in this study introduces a new and more direct route to symmetrically di-substituted cage ligand complexes. ¶ A new range of cobalt(III) surfactant cage complexes, with linear octyl, dodecyl and hexadecyl hydrocarbon chains built directly into the bridgehead structure of the cage ligand, have been prepared by the base catalysed co-condensation of formaldehyde and long chain aliphatic aldehydes with the tripodal cobalt(III) hexaamine complex, [Co(sen)]3+ (sen = 4,4',4''-ethylidynetris(3-azabutan-1-amine)), in acetonitrile solution. Chiral surfactant cage complexes are obtained by capping reactions beginning with the optically pure L-[Co(sen)]3+ precursor complex. The cobalt(III) cage complexes with octyl to hexadecyl substituents are surface active and reduce the surface tension of water to levels approaching those of organic solvents. The dodecyl substituted cage complex forms micelles in aqueous solution when the concentration of cage complex is > 1 ´ 10 -3 mol dm -3 at 25 °C. The cobalt(III) cage head-group of these surfactants undergoes an electrochemically reversible one-electron reduction to the corresponding cobalt(II) cage complex. The reduction potential of the surfactant head group can be tuned to more positive potentials by replacing the bridgehead hydrocarbon chain substituent with an ether linked hydrocarbon chain. The cobalt(III) surfactant-cage complexes are biologically active and are lethal to the tapeworm Hymenolepis diminuta, and the vaginal parasites, Trichomonas vaginalis and Tritrichomonas foetus. The surfactant cage complexes also cause lysis in red-blood cell membranes at concentrations as low 10 -5 mol dm -3 . Their biological activity is linked to the high head-group charge (3+) and size which cause distortions in biological membranes when the membrane is treated with these molecules. The combination of the chemically reversible outer-sphere redox properties of the cobalt cage head-groups and the chirality of the head group introduces a new and possibly unique series of chiral surfactant coordination complexes which are also redox active. ¶ The chiral carboxylic-acid ionophore, lasalocid A, has been used to promote the selective supramolecular transport and extraction of cobalt(III) hexa-aza cage cations and related tripodal cobalt(III) complexes. The conjugate base anion of lasalocid A forms stoichiometric outer-sphere complexes with the cobalt(III) cage and tripod complexes. These outer-sphere complexes are highly lipophilic and partition strongly from water into a chloroform phase. The extraction of the dissymmetric cobalt(III) complexes by the chiral polyether anion is enantioselective for many systems and results in the partial resolution of initially racemic complexes in the aqueous phase. A strong structural preference was demonstrated by the ionophore for symmetrically disubstituted cobalt(III) hexa-aza cage cations with a D-absolute configuration of the ligand about the metal-ion and an R configuration of the coordinated secondary amine N-H groups. The lasalocid A anion was also shown to promote the transport of the complexes, intact, across a chloroform bulk-liquid membrane against an NH4 + concentration gradient. The transport of the cobalt(III) complexes was also enantioselective and resulted in partial resolution of the initially racemic aqueous phase. The most efficiently transported enantiomer of each complex was also the most efficiently extracted isomer in all systems examined, consistent with a transport process limited by interfacial diffusion. The magnitude of the enantiomer separation obtained in some systems was sufficient to indicate that lasalocid A mediated extraction and transport may become a practical method for the resolution of particular types of kinetically-inert chiral metal-amine complexes.

<p>The subject of this thesis is experimental studies of electron-transfer processes in ion-atom collisions at velocities significantly higher than typical orbital velocities of electrons in bound states of atoms or molecules. The experimental technique applied combines the high beam intensity of heavy-ion storage rings with a supersonic gas-jet target equipped with a recoil-ion-momentum spectrometer. In singleelectron capture to fast protons from helium atoms, we have for the first time achieved a complete separation of the kinematic and Thomas transfer mechanisms and are able to perform a quantitative comparison with the many theoretical results on a much more detailed level than what was previously possible. For the process of transfer ionization in proton-helium collisions we have determined the velocity dependence of the Thomas transfer ionization cross section to be the expected<i> v</i><i>p</i>^-11 when the projectile velocity, <i>v</i><i>p</i>, is sufficiently high. Further, we have determined the velocity-dependent probability for shake-off of the second electron from helium provided that the first one is transferred in a kinematic capture process. Finally, we have considered collisions between protons and hydrogen molecules. Here we have found a strong variation in the cross section for transfer and excitation processes when the angle between the direction of the incoming projectile and the internuclear axis of the target molecule is varied. The variation can be explained as a result of quantum mechanical interference related to the two indistinguishable atomic centers of the molecule.</p>

<p>In the society of today the need for alternative energy sources is increasing. The construction of artificial devices for the conversion of sunlight into electricity or fuel seems very attractive from an environmental point of view, since these devices are based on processes that does not necessarily generate any harmful biproducts. In the oxygen evolving photosynthetic process highly efficient energy and electron transfer reactions are responsible for the conversion of the sunlight into chemically stored energy and if the same principles can be used in an artificial device, the only electron supply required, is water. </p><p> This thesis describes energy and electron transfer reactions in supramolecular complexes where the reactions are intended to mimic the basic steps in the photosynthetic process. All complexes are based on ruthenium(II)-trisbipyridine as photosensitizer, that is covalently linked to electron donors or electron or energy acceptors. The photochemical reactions were studied with time resolved transient absorption and emission measurements. In the complexes that mimic the donor side of Photosystem II, where a manganese cluster together with tyrosine catalyses the oxidation of water, intramolecular electron transfer was found to occur from Mn(II) or tyrosine to photo-oxidized Ru(III). Studies of a series of Ru(II)-Mn(II) complexes gave information of the quenching of the Ru(II) excited state by the coordinated Mn(II), which is important for the development of multi-nuclear Ru(II)-Mn complexes. In the supramolecular triad, PTZ-Ru²⁺-Q, the charge separated state, PTZ^+●-Ru²⁺-Q^-●, was rapidly formed, and further development where a second electron acceptor is linked to quinone is planned. Ultra fast energy transfer τ<200 fs), was obtained between ruthenium(II) and osmium(II) in a small artificial antenna fragment. Fast and efficient energy transfer is important in larger antennas or photonic wires where a rapid energy transfer is desired over a large distance.</p>