Biomimetic peptides are autonomously folding secondary structural units designed to serve as models for examining processes that occur in proteins. Although de novo biomimetic peptides are not simply abbreviated versions of proteins already found in nature, designing biomimetic peptides does require an understanding of how native proteins are formed and stabilized. The discovery of autonomously folding fragments of ribonuclease A and tendamistat pioneered the use of biomimetic peptides for determining how the polypeptide sequence stabilizes formation of alpha helices and beta hairpins in aqueous and organic solutions. A set of rules for constructing stable alpha helices have now been established. There is no exact set of rules for designing beta hairpins; however, some factors that must be considered are the identity of the residues in the turn and non-covalent interactions between amino acid side chains. For example, glycine, proline, aspargine, and aspartic acid are favored in turns. Non-covalent interactions that stabilize hairpin formation include salt bridges, pi-stacked aromatic interactions, cation-pi interactions, and hydrophobic interactions. The optimal strand length for beta hairpins depends on the numbers of stabilizing non-covalent interactions and high hairpin propensity amino acids in the specific peptide being designed. Until now, de novo hairpins have not previously been used to examine biological processes aside from protein folding. This thesis uses de novo designed biomimetic peptides as tractable models to examine how non-covalent interactions control the redox properties of tyrosine in enzymes. The data in this study demonstrate that proton transfer to histidine, a hydrogen bond to arginine, and a pi-cation interaction create a peptide environment that lowers the midpoint potential of tyrosine in beta hairpins. Moreover, these interactions contribute equally to control the midpoint potential. The data also show that hydrogen bonding is not the sole determinant of the midpoint potential of tyrosine. Finally, the data suggest that the Tyr 160D2-Arg 272CP47 pi-cation interaction contributes to the differences in redox properties between Tyr 160 and Tyr 161 of photosystem II.

Detailed understanding of electron transfer reactions is important in many aspects of chemistry, biology and solar energy conversion. The main aim of this thesis is to provide further insight into electron transfer through highly conjugated bridge structures. Towards this end, three series of donor-acceptor dyads have been studied, all using an oligo(1,4-phenylene-ethynylene) moiety as the bridge. A common theme in these series is that they explore the effects of having either an ethynylene or phenylene as the attachment group between the bridge and the donor or acceptor. Photophysical characterization of these dyads was carried out by means of time resolved laser spectroscopy. The results show that having an ethynylene as attachment group results in higher rates for bridge mediated electron and energy transfer compared to similar systems, where a phenylene was used. It was also found that most of the investigated systems show a fast back electron transfer. A notable exception is a zinc(II) phthalocyanine- gold(III) porphyrin dyad, where very fast photoinduced electron transfer (kPET = 1.0×1012 s-1) was followed by relatively slow back electron transfer (kBET = 1.0×109 s-1). A complementary DFT investigation indicated that the charge shifted state involves a reduction of the gold ion, rather than the porphyrin ring. This results in lower electronic coupling between the reduced gold porphyrin and the bridge and thus slower back electron transfer. A series of zinc porphyrin platinum acetylide dyads was used to explore the effects on electronic coupling of different attachments points on the porphyrin ring. For the investigated system it was found that linking at the meso-position results in an eight-fold increase in electron transfer rate compared to the β-position. In addition, a series of mixed valence compounds was used to investigate electronic coupling mediated by cross-hyperconjugated or cross-π-conjugated bridges. The results indicate coupling elements of 100-400 cm-1, with the cross-π-conjugated bridge having the largest coupling. A complementary TD-DFT study indicates that both through bond and through space coupling can be active in these systems. The relative contribution of these two mechanisms to the electronic coupling is highly conformer dependent.

This thesis examines the synthesis of conformationally constrained β-amino acids and β- peptides, and the electron transfer properties of the latter when immobilised on gold. Additionally, cross metathesis on gold was investigated as a method for surface functionalisation. Chapter One introduces the concepts of electron transfer in nature, how it is facilitated by the secondary structure in α-peptides, and why β-peptides might be useful for studying electron transfer. This is followed by a discussion of the properties of β-peptides, including the enhanced stability and variety of helical secondary structures and the greater potential for functionalisation of the peptide backbone when compared to α-peptides. Finally, the conformational constraints of ring-systems on cyclic amino acids is discussed, with reference to the stabilising effect of these compounds on peptide secondary structures. Chapter Two describes the electrochemical analysis of β-hexapeptides immobilised on gold. The chapter is prefaced by a discussion of the important electron transfer mechanisms for peptides, the fabrication of peptide-gold self-assembled monolayer (SAM) interfaces, and the electron transfer in helical α-peptides. β-Peptides containing an electroactive ferrocene moeity were immobilised on gold and studied using cyclic voltammetry and chronoamperometry. The latter method was used to examine the dependence of the electron transfer rate on overpotential, thereby determining the likely mode of electron transfer through the β-peptides SSβ₆Fc, Fcβ₆SS and SC₁₅β₆Fc. These peptides exhibited very weak dependence on overpotential, characteristic of electron transfer behaviour of an electron hopping mechanism (which is also thought to occur in helical α-peptides). Both the dipole moment of the peptides and the structure of the sulfurlinker group were found to be important in determining the rate of electron transfer. Conversely, the equivalent α-peptide SSα₆Fc exhibited electron transfer behaviour characteristic of the less efficient tunnelling mechanism, which is thought to operate in strand-like peptides. Chapter Three examines the application of cross metathesis, using a Grubbs' second generation catalyst, as a means to functionalise olefin-terminated self-assembled monolayers on gold. Abstract iv Firstly, an introduction into the limited published research on cross metathesis on both planar surfaces and nanoparticles is given. Olefin-terminated thiol 3.18, suitable for immobilisation on gold, and solution phase olefin-terminated ferrocene 3.10 were synthesised as reactants for cross metathesis studies. An analytical methodology was developed involving the cross metathesis of surface-immobilised 3.18 with ferrocene 3.10 in dichloromethane, whereby the concentration of electroactive cross metathesis product 3.22 was monitored electrochemically as a function of time. The concentration of surface-immobilised product 3.22 was determined by integration of the oxidation peak area and found to be highly dependent on both the concentration of immobilised olefin reactant 3.18 and reaction time. Furthermore, the surface concentration of ferrocenyl model disulfide 3.21 and thiol 2.18 decayed markedly upon addition of Grubb's catalyst, as revealed by the decrease in the oxidation peak area, which suggested that catalystmediated desorption was occurring. Chapter Four details the solution-phase synthesis of ferrocene- and thiol-functionalised β- hexapeptides used in both the electron transfer studies described in chapter two, and in the determination of secondary structure using circular dichroism and NMR techniques. The synthesis of simple model compounds 4.14, 4.16 and 4.18 established the incompatibility of the deprotection of methyl and benzyl ester protecting groups with protected-thiol and disulfide linkers, leading to the use of N-hydroxysuccinmide-activated sulfur-linkers 4.20 and 4.22 in further synthesis. A number of β-hexapeptides were synthesised by amide coupling of β- tripeptides functionalised at the N- and C-termini. Structural studies of the methanol soluble β- hexapeptide 4.60 suggested that the covalent attachment of ferrocene moeity to the C-terminus of a β-peptide did not disrupt the formation of a 14-helix in solution. β-peptides containing functionality at both the C- and N-termini (such as SSβ₆Fc, SSβ₆Et and acetyl-protected SC₁₅β₆Fc) were not suitable for solution phase structural studies; however, molecular modelling suggested that helical conformations are the most stable these β-peptides in solution phase. Chapter Five outlines the synthesis of novel cyclic β-amino acids by two different general synthetic routes. The first uses an efficient conjugate addition/fluorination reaction of α,β- unsaturated esters with lithiated chiral secondary amines to prepare the novel cyclopentyl- and cyclohexyl-based fluorinated β-amino acids 2.43a and 2.43b. The high diastereoselectivity of this reaction, which introduces two stereocentres into the achiral unsaturated esters, is directed by the configuration of the attacking amine. The second methodology utilizes the versatile ringclosing metathesis reaction in the synthesis of novel cyclic β-amino acids. A stereoselective Abstract v trans-alkylation of olefinic β-amino acids gave the required β-dienes 5.62 and 5.77. Optimised cyclisation yields were achieved with a Grubb's 2nd generation catalyst for diene 5.62 and Grubb's 1st generation catalyst for diene 5.77, to give the trans-cycloheptyl- and cyclooctylbased β-amino acids 5.63 and 5.78, respectively. The attempted synthesis of cyclononyl-based β-amino acid 5.87 using both catalysts yielded only cyclic dimer products 5.88 and 5.89. The trans configuration of the 5.62 diene was confirmed by x-ray crystallography. Chapter Six is an experimental chapter and outlines the electrochemical setup and analysis, and the synthesis, purification and characterisation of compounds described in this thesis.

No description available.

abstract: The photosynthetic reaction center is a type of pigment-protein complex found widely in photosynthetic bacteria, algae and higher plants. Its function is to convert the energy of sunlight into a chemical form that can be used to support other life processes. The high efficiency and structural simplicity make the bacterial reaction center a paradigm for studying electron transfer in biomolecules. This thesis starts with a comparison of the primary electron transfer process in the reaction centers from the Rhodobacter shperoides bacterium and those from its thermophilic homolog, Chloroflexus aurantiacus. Different temperature dependences in the primary electron transfer were found in these two type of reaction centers. Analyses of the structural differences between these two proteins suggested that the excess surface charged amino acids as well as a larger solvent exposure area in the Chloroflexus aurantiacus reaction center could explain the different temperature depenence. The conclusion from this work is that the electrostatic interaction potentially has a major effect on the electron transfer. Inspired by these results, a single point mutant was designed for Rhodobacter shperoides reaction centers by placing an ionizable amino acid in the protein interior to perturb the dielectrics. The ionizable group in the mutation site largely deprotonated in the ground state judging from the cofactor absorption spectra as a function of pH. By contrast, a fast charge recombination assoicated with protein dielectric relaxation was observed in this mutant, suggesting the possibility that dynamic protonation/deprotonation may be taking place during the electron transfer. The fast protein dielectric relaxation occuring in this mutant complicates the electron transfer pathway and reduces the yield of electron transfer to QA. Considering the importance of the protein dielectric environment, efforts have been made in quantifying variations of the internal field during charge separation. An analysis protocol based on the Stark effect of reaction center cofactor spectra during charge separation has been developed to characterize the charge-separated radical field acting on probe chromophores. The field change, monitored by the dynamic Stark shift, correlates with, but is not identical to, the electron transfer kinetics. The dynamic Stark shift results have lead to a dynamic model for the time-dependent dielectric that is complementary to the static dielectric asymmetry observed in past steady state experiments. Taken together, the work in this thesis emphasizes the importance of protein electrostatics and its dielectric response to electron transfer. / Dissertation/Thesis / Ph.D. Physics 2012

No description available.

Orientador: Prof. Dr. Fernando Heering Bartoloni / Dissertação (mestrado) - Universidade Federal do ABC. Programa de Pós-Graduação em Ciência e Tecnologia/Química, 2016. / No presente trabalho, foram feitos estudos cineticos empregando lofina, bem como alguns derivados desta, como ativadores (ACTs) da reacao quimiluminescente peroxioxalato, com o objetivo de avaliar se tais compostos alteram o mecanismo de reacao. Foi possivel obter valores medios para as constantes de velocidade kobs 1 = (3,1 } 0,5) ~ 10.3 s.1 e kobs 2 = (3,0 } 0,1) ~ 10.1 s.1!para todos os ACTs estudados, entre eles o 9,10-difenilantraceno, rubreno e perileno, ativadores comumente empregados, indicando que tais compostos nao influenciam nas etapas lentas da transformacao. Adicionalmente, foram obtidos valores medios para as constantes de velocidade bimolecular de k1(2) = (1,9 } 0,5) L mol.1 s.1 e trimoleculares de k1(3) =(9,5 } 0,4) ~ 102 L2 mol.2 s.1 e k2(3) = (3 } 2) ~ 104 L2 mol.2 s.1, associadas a etapas especificas do mecanismo, sendo que estes estao de acordo com os reportados anteriormente na literatura. Alem disso, buscou-se evidencias cineticas da interacao entre a base catalisadora imidazol e o Intermediario de Alta Energia (IAE) desta reacao, por um processo de decomposicao escura, que reduz o rendimento de emissao da reacao. Os valores obtidos para a constante de velocidade associada a decomposicao termica unimolecular do IAE (kD1) variaram significativamente com diferentes ACTs (entre 10.1¿Y102 s.1); eram esperados valores proximos para esta constante de velocidade, nao sendo possivel determinar um valor medio para tal no momento. O valor medio de kD2 = (3 } 1) ~ 104 L mol.1 s.1 foi obtido para a decomposicao 10 bimolecular do IAE por IMI-H, indicando que imidazol e tao eficiente quanto perileno na decomposicao do IAE, sendo mais eficiente do que 9,10-difenilantraceno mas menos eficiente do que rubreno. Ademais, foi observado que lofina e seus derivados, quando utilizados como ativadores, podem ser tao eficientes no processo de decomposicao do IAE da reacao peroxioxalato quanto o ativador classico rubreno, sendo mais eficientes do que perileno e 9,10-difenilantraceno. O rendimento quantico maximo de formacao de estados excitados singlete (¿³S ¿) se manteve constante no intervalo de concentracao de imidazol estudado, indicando que a quantidade total de IAE gerado em solucao e independente da concentracao desta base. Em seguida, investigou-se a possibilidade da geracao de estados excitados ocorrer por meio de um processo de tranferencias de proton e eletron acopladas (PCET). Isto se daria por uma transferencia de eletron intermolecular do ACT para o IAE, concertada com uma transferencia de proton intramolecular, entre a hidroxila fenolica e o nitrogenio imidazolico da propria molecula de determinados derivados de lofina. Uma outra possibilidade e a de que um derivado de lofina que possui um grupo OH distante do nitrogenio imidazolico realize uma transferencia de proton intermolecular, para uma molecula de IMI-H externa. Entretanto, os resultados obtidos demonstram que a reacao de transferencia de eletron, envolvida na etapa inicial do processo de quimiexcitacao, e uma transferencia de eletron convencional, equivalente a envolvida quando na presenca de ACTs classicos. Em altas concentracoes de IMI-H, os valores de ¿³S¿ reduzem significativamente, indicando que outras reacoes que nao levam ao IAE passam a ser significativas nestas condicoes. / In this work, kinetic studies were performed using lophine, and some of its derivatives, as activators (ACTs) of the chemiluminescent peroxyoxalate reaction, in order to evaluate if such compounds are able to alter the reaction mechanism. Main values were obtained for the observed rate constants, being kobs 1 = (3,1 } 0,5) ~ 10.3 s.1 and kobs 2 = (3,0 } 0,1) ~ 10.1 s.1; these were determined for all activators, including 9,10-diphenylanthracene, rubrene and perylene, which are commonly used activators, indicating that the studied compounds do not participate in the rate limiting steps of this transformation. Moreover, mean values were obtained for the bi (k1(2) = (1,9 } 0,5) L mol.1 s.1) and trimolecular (k1 (3) = (9,5 } 0,4) ~ 102 L2 mol.2 s.1 e k2 (3) = (3 } 2) ~ 104 L2 mol.2 s.1) rate constants associated to the mechanism; these are in agreement with values previously reported on the literature. Besides, kinetic evidences were acquired for the interaction between the basic catalyst imidazole and the High Energy Intermediate (HEI) of this reaction, through a dark decomposition process, which is capable of reducing the light emission yield of the reaction. Values obtained for the rate constant associated to the unimolecular thermal decomposition of the HEI (kD1) differed significantly among ACTs, spanning from 10.1 to 102 s.1. Similar values were expected for this rate constant, thus, it was not possible to determine a mean value for it, at the moment. A mean value of kD 2 =(3 } 1) ~ 104 L mol-1 s-1 was obtained for the bimolecular decomposition rate constant of the HEI by imidazole, showing that this base is as efficient as perylene in decomposing the HEI, being more efficient than 9,10-diphenylanthracene but less 12efficient than rubrene. Moreover, it was observed that lophine and its derivatives, when used as activators, can be as efficient as rubrene in decomposing the HEI, being more efficient than perylene and 9,10-diphenylanthracene. The maximum yield for singlet excited states formation (¿³S¿) remained constant in the studied range of imidazole concentration, indicating that the total amount of generated HEI in solution does not depend on the concentration of this catalyst. Next, the possibility of generation of excited states through a proton-coupled electron transfer (PCET) process was investigated. This could occur, for certain lophine derivatives, by an intermolecular electron transfer from the ACT to the HEI, concerted with an intramolecular proton transfer, from the phenolic hydroxyl group to the imidazolic nitrogen within the molecule. Another possibility, for lophine derivatives which bear the OH group distant from the imidazolic nitrogen, is to the proton transfer to occur intermolecularly, to an external imidazole molecule. However, the obtained results indicate that the electron transfer reaction, involved on the initial step of the chemiexcitation process, is a typical one, equivalent to the electron transfer reaction operating with classical ACTs. At high imidazole concentrations, values for ¿³S ¿reduced drastically, indicating that secondary reactions that do not generate the HEI become significant at these conditions.

abstract: Photosystem I (PSI) is a multi-subunit, pigment-protein complex that catalyzes light-driven electron transfer (ET) in its bi-branched reaction center (RC). Recently it was suggested that the initial charge separation (CS) event can take place independently within each ec2/ec3 chlorophyll pair. In order to improve our understanding of this phenomenon, we have generated new mutations in the PsaA and PsaB subunits near the electron transfer cofactor 2 (ec2 chlorophyll). PsaA-Asn604 accepts a hydrogen bond from the water molecule that is the axial ligand of ec2B and the case is similar for PsaB-Asn591 and ec2A. The second set of targeted sites was PsaA-Ala684 and PsaB-Ala664, whose methyl groups are present near ec2A and ec2B, respectively. We generated a number of mutants by targeting the selected protein residues. These mutations were expected to alter the energetics of the primary charge separation event. The PsaA-A684N mutants exhibited increased ET on the B-branch as compared to the A-branch in both in vivo and in vitro conditions. The transient electron paramagnetic resonance (EPR) spectroscopy revealed the formation of increased B-side radical pair (RP) at ambient and cryogenic temperatures. The ultrafast transient absorption spectroscopy and fluorescence decay measurement of the PsaA-A684N and PsaB-A664N showed a slight deceleration of energy trapping. Thus making mutations near ec2 on each branch resulted into modulation of the charge separation process. In the second set of mutants, where ec2 cofactor was target by substitution of PsaA-Asn604 or PsaB-Asn591 to other amino acids, a drop in energy trapping was observed. The quantum yield of CS decreases in Asn to Leu and His mutants on the respective branch. The P700 triplet state was not observed at room and cryogenic temperature for these mutants, nor was a rapid decay of P700+ in the nanosecond timescale, indicating that the mutations do not cause a blockage of electron transfer from the ec3 Chl. Time-resolved fluorescence results showed a decrease in the lifetime of the energy trapping. We interpret this decrease in lifetime as a new channel of excitation energy decay, in which the untrapped energy dissipates as heat through a fast internal conversion process. Thus, a variety of spectroscopic measurements of PSI with point mutations near the ec2 cofactor further support that the ec2 cofactor is involved in energy trapping process. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2014

abstract: This thesis develops molecular models for electron transport in molecular junctions and intra-molecular electron transfer. The goal is to identify molecular descriptors that afford a substantial simplification of these electronic processes. First, the connection between static molecular polarizability and the molecular conductance is examined. A correlation emerges whereby the measured conductance of a tunneling junction decreases as a function of the calculated molecular polarizability for several systems, a result consistent with the idea of a molecule as a polarizable dielectric. A model based on a macroscopic extension of the Clausius-Mossotti equation to the molecular domain and Simmon’s tunneling model is developed to explain this correlation. Despite the simplicity of the theory, it paves the way for further experimental, conceptual and theoretical developments in the use of molecular descriptors to describe both conductance and electron transfer. Second, the conductance of several biologically relevant, weakly bonded, hydrogen-bonded systems is systematically investigated. While there is no correlation between hydrogen bond strength and conductance, the results indicate a relation between the conductance and atomic polarizability of the hydrogen bond acceptor atom. The relevance of these results to electron transfer in biological systems is discussed. Hydrogen production and oxidation using catalysts inspired by hydrogenases provides a more sustainable alternative to the use of precious metals. To understand electrochemical and spectroscopic properties of a collection of Fe and Ni mimics of hydrogenases, high-level density functional theory calculations are described. The results, based on a detailed analysis of the energies, charges and molecular orbitals of these metal complexes, indicate the importance of geometric constraints imposed by the ligand on molecular properties such as acidity and electrocatalytic activity. Based on model calculations of several intermediates in the catalytic cycle of a model NiFe complex, a hypothetical reaction mechanism, which very well agrees with the observed experimental results, is proffered. Future work related to this thesis may involve the systematic analysis of chemical reactivity in constrained geometries, a subject of importance if the context of enzymatic activity. Another, more intriguing direction is related to the fundamental issue of reformulating Marcus theory in terms of the molecular dielectric response function. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2015

abstract: Sunlight, the most abundant source of energy available, is diffuse and intermittent; therefore it needs to be stored in chemicals bonds in order to be used any time. Photosynthesis converts sunlight into useful chemical energy that organisms can use for their functions. Artificial photosynthesis aims to use the essential chemistry of natural photosynthesis to harvest solar energy and convert it into fuels such as hydrogen gas. By splitting water, tandem photoelectrochemical solar cells (PESC) can produce hydrogen gas, which can be stored and used as fuel. Understanding the mechanisms of photosynthesis, such as photoinduced electron transfer, proton-coupled electron transfer (PCET) and energy transfer (singlet-singlet and triplet-triplet) can provide a detailed knowledge of those processes which can later be applied to the design of artificial photosynthetic systems. This dissertation has three main research projects. The first part focuses on design, synthesis and characterization of suitable photosensitizers for tandem cells. Different factors that can influence the performance of the photosensitizers in PESC and the attachment and use of a biomimetic electron relay to a water oxidation catalyst are explored. The second part studies PCET, using Nuclear Magnetic Resonance and computational chemistry to elucidate the structure and stability of tautomers that comprise biomimetic electron relays, focusing on the formation of intramolecular hydrogen bonds. The third part of this dissertation uses computational calculations to understand triplet-triplet energy transfer and the mechanism of quenching of the excited singlet state of phthalocyanines in antenna models by covalently attached carotenoids. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016