Tyrosyl radicals can facilitate proton-coupled electron transfer (PCET) reactions that are linked to catalysis in many biological systems. One such protein system is ribonucleotide reductase (RNR). This enzyme is responsible for the conversion of ribonucleotides to deoxyribonucleotides. The beta2 subunit of class Ia RNRs contains a diiron cluster and a stable tyrosyl radical (Y122*). Reduction of ribonucleotides is dependent on reversible, long-distance PCET reactions involving Y122* located 35 Å from the active site. Protein conformational dynamics are postulated to precede diiron cluster assembly and PCET reactions in RNR. Using UV resonance Raman spectroscopy, we identified structural changes to histidine, tyrosine, and tryptophan residues with metal cluster assembly in beta2. With a reaction-induced infrared spectroscopic technique, local amide bond structural changes, which are associated with the reduction of Y122*, were observed. Moreover, infrared spectroscopy of tyrosine-containing pentapeptide model compounds supported the hypothesis that local amide bonds are perturbed with tyrosyl radical formation. These findings demonstrate the importance of the amino acid primary sequence and amide bonds on tyrosyl radical redox changes. We also investigated the function of a unique tyrosine-histidine cross-link, which is found in the active site of cytochrome c oxidase (CcO). Spectrophotometric titrations of model compounds that mimic the cross-link were consistent with a proton transfer role in CcO. Infrared spectroscopic data support the formation of tyrosyl radicals in these model compounds. Collectively, the effect of the local structure and the corresponding protein dynamics involved in tyrosyl radical-mediated PCET reactions are illustrated in this work.

Biological processes at the cellular level take place in heterogeneous environments, and usually involve only a small number of molecules. They tend to exhibit strong time dependent fluctuations, as a result, and are, therefore, intrinsically stochastic. The present thesis describes some of the efforts I have made during the course of my research work to develop simple, analytically tractable models of a selection of biologically-inspired problems in which this kind of stochasticity is a central ingredient. These problems are: (i) single molecule enzyme activity (ii) intermittency in single enzymes, (iii) liquids crystal dynamics (iv) modulation of electron transfer kinetics during photosynthesis, and (v) anomalous polymer translocation dynamics. All of these problems can be defined in terms of quantity that changes randomly in time because of environmental fluctuations with broad distributions of relaxation times. In this thesis I show that a generalization of a model that describes simple Brownian Motion can be used to understand many of the dynamical aspects of these problems.

Denitrification is an anaerobic process performed by several soil bacteria as an alternative to aerobic respiration. A key-step in denitrification (the N-N-bond is made) is catalyzed by nitric oxide reductase (NOR); 2NO + 2e- + 2H+ → N2O + H2O. NOR from Paracoccus denitrificans is a member of the heme copper oxidase superfamily (HCuOs), where the mitochondrial cytochrome c oxidase is the classical example. NOR is situated in the cytoplasmic membrane and can, as a side reaction, catalyze the reduction of oxygen to water. NORs have properties that make them divergent members of the HCuOs; the reactions they catalyze are not electrogenic and they do not pump protons. They also have five strictly conserved glutamates in their catalytic subunit (NorB) that are not conserved in the ‘classical’ HCuOs. It has been asked whether the protons used in the reaction really come from the periplasm and if so how do the protons proceed through the protein into the catalytic site? In order to find out whether the protons are taken from the periplasm or the cytoplasm and in order to pinpoint the proton-route in NorB, we studied electron- and proton transfer during a single- as well as multiple turnovers, using time resolved optical spectroscopy. Wild type NOR and several variants of the five conserved glutamates were investigated in their solubilised form or/and reconstituted into vesicles. The results demonstrate that protons needed for the reaction indeed are taken from the periplasm and that all but one of the conserved glutamates are crucial for the oxidative phase of the reaction that is limited by proton uptake to the active site. In this thesis it is proposed, using a model of NorB, that two of the glutamates are located at the entrance of the proton pathway which also contains two of the other glutamates close to the active site.

Many anticancer therapies are based on the interaction of small molecule drugs with nucleic acids, particularly DNA. Electrospray ionization tandem mass spectrometry has established itself as an irreplaceable tool for the characterization of DNA adducts produced by alkylating agents, carcinogens, and antitumor drugs, in addition to the characterization of nucleic acid post-transcriptional modifications. ESI-MS was used to assess the non-covalent binding of a novel series of intercalating anthrapyrazoles to duplexes containing different sequences. Relative binding affinities paralleled the shift in melting point of the DNA duplexes measured from a previous study. Upon collisionally induced dissociation of the duplex/anthrapyrazole complexes, different binding strengths were discerned based on the fragmentation patterns. In addition, the interactions of a new series of sulfur-containing acridine ligands, some that functioned as alklyating mustards, with duplex DNA were also evaluated. Non-covalent and covalent binding of each ligand was determined, and the site of adduction (G > A) was revealed for the covalent modifications. The distribution of cross-linked products and mono-adducts by psoralen analogs was also monitored by both LC-UV and IRMPD-MS methods. Reactions at 5’-TA sites were favored over 5’-AT sites. The sites of interstrand cross-linking were determined by fragmentation of the duplex/psoralen complexes by infrared multiphoton dissociation (IRMPD). Ultraviolet photodissociation (UVPD) at 193 nm caused efficient charge reduction of deprotonated oligodeoxynucleotides via electron detachment. Subsequent CID of the charge-reduced oligodeoxynucleotides formed upon electron detachment, in a net process called electron photodetachment dissociation (EPD), resulted in a diverse array of abundant sequence ions which allowed the modification site(s) of three modified oligodeoxynucleotides to be pinpointed to a more specific location than by conventional CID. Electron transfer dissociation (ETD) caused efficient charge reduction of multi-protonated oligonucleotides. Subsequent CAD of the charge-reduced oligonucleotides formed upon electron transfer, in a net process termed electron transfer collision activated dissociation (ETcaD), resulted in rich backbone fragmentation, with a marked decrease in the abundance of base loss ions and internal fragments. ETcaD of an oligonucleotide duplex resulted in specific backbone cleavages, with conservation of weaker non-covalent bonds. In addition, IRMPD and UVPD were used to activate charge-reduced oligonucleotides formed upon electron transfer. ET-IRMPD afforded tunable characterization of the modified DNA and RNA, allowing for modified bases to be directly analyzed. ET-UVPD promoted higher energy backbone fragmentation pathways and created the most diverse MS/MS spectra. The numerous products generated by the hybrid MS/MS techniques (ETcaD, ET-IRMPD, and ET-UVPD) resulted in specific and extensive backbone cleavages which allowed for the modification sites of multiple oligonucleotides to be pinpointed. / text

This dissertation has focused on i) optimizing charge transfer rates at indium-tinoxide (ITO) electrodes, and ii) characterization of the supramolecular structure and properties of ultra thin surface modifier films on modified electrodes for various device applications. Commercial ITO surfaces were modified using conducting polymer thin film architectures with and without various chemical activation procedures. Ferrocene derivatives were used as redox probes, which showed dramatic changes in electron transfer rate as the SA-PANI/PAA layers were added to the ITO surface. Highest rates of electron transfer were observed for DMFc, whose oxidation potential coincides with the potential region where these SA-PANI/PAA films reach their optimal electroactivity. Apparent heterogeneous electron transfer rate constants, kS, measured voltammetrically, were ca.10 x higher for SA-PANI/PAA films on ITO, versus clean ITO substrates. These films also showed linear potentiometric responses with retention of the ITO transparency with the capability to create smoothest films using an aqueous deposition protocol, which proved important in other applications. ITO electrodes were also modified via chemisorption of carboxy functionalized EDOTCA and electropolymerization of PEDOTCA/PEDOT copolymers, when properly optimized for thickness and structure, enhance voltammetrically determined electron transfer rates (kS) to solution probe molecules, such as dimethylferrocene (DMFc). Values of kS ≥ 0.4 cm•sec⁻¹, were determined, approaching rates seen on clean gold surfaces. ITO activation combined with formation of these co-polymer films has the effect of enhancing the electroactive fraction of electrode surface, versus a non-activated, unmodified ITO electrode, which acts as a “blocked” electrode. The electroactivity and spectroelectrochemistry of these films helped to resolve the electron transfer rate mechanism and enabled the construction of models in combination with AFM, XPS, UPS and RAIRS studies. The surface topography, structure, composition, work function and contact angle, also revealed other desirable properties for molecular electronic devices. The carboxylic functionality of the EDOTCA molecule adds more desirable properties compared to normal PEDOT films, such as favoring the deposition of smooth films, increasing the optical contrast, participating in hydrogen-bonding, chemisorption to oxide surface, self-doping and providing a linker for incorporation of different functional groups, new molecules, or nanoparticles. Periodic sub-micron electrode arrays can be created using micro-contact printing and electropolymerization. The sinusoidal modulation of the refractive index of such confined conducting polymer nanostructures or nanoparticle stripes allows efficient visible light diffraction. The modulation of the diffraction efficiency at PANI and PEDOT gratings in the presence of an analytical stimulus such as pH or potential demonstrate the sensing capability at these surfaces. The template stripped gold surfaces that are being developed in our lab demonstrate several advantages over commercially available evaporated gold films especially for nanoscale surface modification.

Photoinduced electron transfer is involved in a number of photochemical and photobiological processes. One example of this is photosynthesis, where the absorption of sunlight leads to the formation of charge-separated states by electron transfer. The redox equivalents built up by successive photoabsorption and electron transfer is further used for the oxidation of water and reduction of carbon dioxide to sugars. The work presented in this thesis is part of an interdisciplinary effort aiming at a functional mimic of photosynthesis. The goal of this project is to utilize sunlight to produce renewable fuels from sun and water. Specifically, this thesis concerns photoinduced electron transfer in donor(D)-photosensitizer(P)-acceptor(A) systems, in mimic of the primary events of photosynthesis. The absorption of a photon typically leads to transfer of a single electron, i.e., charge separation to produce a single electron-hole pair. This fundamental process was studied in several molecular systems. The purpose of these studies was optimization of single electron transfer as to obtain charge separation in high yields, with minimum losses to competing photoreactions such as energy transfer.Also, the lifetime of the charge separated state and the confinement of the electron and hole in three-dimensional space are important in practical applications. This led us to explore molecular motifs for linear arrays based on Ru(II)bis-tridentate and Ru(II)tris-bidentate complexes. The target multi-electron catalytic reactions of water-splitting and fuel production require a build-up of redox equivalents upon successive photoexcitation and electron transfer events. The possibilities and challenges associated with such processes in molecular systems were investigated. One of the studied systems was shown to accumulate two electrons and two holes upon two successive excitations, without sacrificial redox agents and with minimum yield losses. From these studies, we have gained better understanding of the obstacles associated with step-wise photoaccumulation of charge and how to overcome them.

No description available.

No description available.

Copper is an essential trace element for living organisms and has both known and additional suspected roles in human health and disease. The current understanding of copper metabolism is substantial but incomplete, particularly in regard to storage and exchange at the subcellular level, although available evidence indicates exchangeable intracellular copper is in the monovalent oxidation state. Selective fluorescent probes with sufficient sensitivity to detect Cu(I) availability at physiologically relevant levels and at subcellular resolution would be valuable tools for studying copper metabolism. As a contribution toward this goal, this work describes the development of Cu(I)-selective fluorescent probes with greatly improved aqueous solubility, contrast ratio, and fluorescence quantum yield. This work also describes the development of water-soluble, 1:1-binding chelators that form colorless, air-stable copper(I)-complexes. By acting as copper(I) buffering agents and affinity standards, these compounds can serve a complementary role to fluorescent probes in the study of copper biochemistry.

EPR spectroscopy and isotopic substitution were used to gain increased knowledge about the proton-coupled electron transfer (PCET) mechanism for the reduction of the tyrosine D radical (YD*) in photosystem II. pL dependence (where pL is either pH or pD) of both the rate constant and kinetic isotope effect (KIE) was examined for YD* reduction. Second, the manner in which protons are transferred during the rate-limiting step for YD* reduction at alkaline pL was determined. Finally, high field electron paramagnetic resonance (EPR) spectroscopy was used to study the effect of pH on the environment surrounding both the tyrosine D radical and the tyrosine Z radical (YZ*). At alkaline pL, it was determined that the proton and electron are both transferred in the rate-limiting step of YD* reduction. At acidic pL, the proton transfer occurs first followed by electron transfer. Proton inventory experiments indicate that there is more than one proton donation pathway available to YD* during PCET reduction at alkaline pL. Additionally, the proton inventory experiments indicate that at least one of those pathways is multiproton. High field EPR experiments indicate that both YD* and YZ* are hydrogen bonded to neutral species. The EPR gx component for YD* is invariant with respect to pH. Analysis of the EPR gx component for Yz* indicates that its environment becomes more electropositive as the pH is increased. This is most likely due to changes in the hydrogen bond strength