No / The reactions of ionised pyridazine, aminopyrazine and aminopyridine and the corresponding ¿-distonic ions are examined by a combination of tandem mass spectrometric techniques, including analysis of metastable ion (MI), collision induced dissociation and neutralisation¿reionisation mass spectra (NRMS). Further insight into the relative stability and energy barriers towards tautomerism of each ionised heterocycle with its ¿-distonic isomer is obtained by computational methods. In all these systems, both the conventional radical-cation and the ¿-distonic tautomer are stable species which exist in discrete energy wells, with a significant barrier towards their interconversion. Although each ¿-distonic ion is sufficiently stable to survive neutralisation¿reionisation, the conventional ionised heterocycle is more stable in each case. The possibility of investigating proton-transport catalysis in the tautomerism of these ionic systems is discussed.

The research described in this thesis employs a variety of Electron Paramagnetic Resonance (EPR) techniques for the study of the electronic and structural properties of artificial supramolecular porphyrin systems and of protein complexes of biological relevance. The electron delocalisation in the cationic radical and photoexcited triplet states of linear and cyclic Π-conjugated multiporphyrin arrays was investigated. In the radical cations, information on the extent of delocalisation can be inferred from the measurement of hyperfine couplings, either indirectly from the continuous wave EPR spectrum or directly using pulsed hyperfine EPR techniques. The results of room temperature EPR experiments showed complete delocalisation of the electron on the timescale of the EPR experiments, but frozen solution EPR measurements revealed localisation onto mainly two to three porphyrin units in the larger porphyrin systems. Information on the delocalisation of the triplet state in the same porphyrin systems is contained both in the hyperfine couplings and in the zero-field splitting (ZFS) interaction. The results outlined in this thesis show that the hyperfine couplings provide a much more accurate estimate of the extent of delocalisation. The trends in proton and nitrogen hyperfine couplings with the size of the porphyrin systems indicate uneven spin density distributions over the linear arrays, but complete delocalisation in the cyclic systems. Time-resolved EPR and magnetophotoselection experiments have shown a reorientation of the zero-field splitting tensor between a single porphyrin unit and longer linear arrays, resulting in alignment of the main optical transition moment and the Z axis of the ZFS tensor. Continuous wave and pulsed dipolar EPR techniques were employed for the determination of the structure of two different protein complexes, the homomultimeric twin-arginine translocase A (TatA) protein channel and the ferredoxin-P450 complex of the electron transport chain in Novosphingobium aromaticivorans. The interaction between nitroxide spin labels introduced at different positions of the TatA monomer was investigated in the complex reconstituted in detergent micelles by analysing the dipolar broadening of the EPR spectra and the results of three- and four-pulse Double Electron-Electron Resonance (DEER) measurements. In combination with results from NMR and molecular dynamics calculations, a structure for the channel complex was proposed. The structure of the ferredoxin-cytochrome P450 complex was investigated by orientation-selective DEER between nitroxide labels introduced on the cytochrome P450 protein and the iron-sulfur cluster of the ferredoxin. The distance and orientation information contained in the experimental DEER data was interpreted in terms of a structural model of the protein complex by orientation-selective DEER simulations combined with a modelling approach based on protein-protein docking.

Guanine is generally accepted as the most easily oxidized DNA base when cells are subjected to ionizing radiation, photoionization or photosensitization. At pH 7, the midpoint reduction potential is on the order of 0.2 – 0.3 V higher than those of the radicals of e.g. tyrosine, tryptophan cysteine and histidine, so that the radical “repair” (or at least, a thermodynamically favorable reaction) involving these amino acids is feasible. Computational quantum studies have been done on tyrosine, tryptophan, cysteine and histidine side chains as they appear in histones. Density functional theory was employed using B3LYP/6-31G+ (d, p) basis set to study spin densities on these amino acids side chains as they pair with the guanine radical cation. The amino acid side chains are positioned so as not to disrupt the Watson-Crick base pairing. Our results indicate that, these side chains of amino acid with reducing properties can repair guanine radical cation through electron transfer coupled with proton transfer.

Long-distance radical cation transport was studied in DNA condensates where linearized pUC19 plasmid was ligated to an oligomer and transformed into DNA condensates with spermidine. DNA condensates were detected by Dynamic Light Scattering and observed by Transmission Electron Microscopy. Introduction of charge into the condensates causes long-distance charge migration, which is detected by reaction at the remote guanines. The efficiency of charge migration in the condensate is significantly less than it is for the corresponding oligomer in solution. This result is attributed to a lower mobility for the migrating radical cation in the condensate, caused by inhibited formation of charge-transfer-effective states. Radical cation transport was also studied in DNA condensates made from an oligomer sandwiched between two linearized plasmids by double ligation. Unlike the single ligated plasmid condensates, the efficiency of charge migration in the double ligated plasmid-condensates is high, indicative of local structural and conformational transformation of the DNA duplexes. Organic monomer units having extended ð-conjugation as part of a long conducting polymer was synthesized and characterized. The monomer units were covalently attached to particular positions in DNA oligonucleotides by either the convertible nucleotide approach or by phosphoramidite chemistry. Successful attachment of the monomer units to DNA were confirmed by mass spectral analysis. The DNA-conjoined monomer units can self assemble in the presence of complementary sequences which act as templates that can control polymer formation and structure. By this method the para-direction of the polymer formation can be enforced and may be used to generate materials having nonrecurring, irregular structures.

This work presents a new implementation of the QP algorithm, a computer method to diagonalize the extremely large matrices arising in multimode vibronic problems. Benchmark calculations are included, showing the accuracy of the program. The QP algorithm is extended to treat multiple electronic surfaces for competitive control and this is demonstrated with an Hamiltonian including three electronic states, a model of the benzene radical cation. Finally, the evolution of zeroth-order states in a simple two electronic states, two dimensional model with a conical intersection is explored, towards building a time-dependent view of overlapping resonances coherent control.

This work presents a new implementation of the QP algorithm, a computer method to diagonalize the extremely large matrices arising in multimode vibronic problems. Benchmark calculations are included, showing the accuracy of the program. The QP algorithm is extended to treat multiple electronic surfaces for competitive control and this is demonstrated with an Hamiltonian including three electronic states, a model of the benzene radical cation. Finally, the evolution of zeroth-order states in a simple two electronic states, two dimensional model with a conical intersection is explored, towards building a time-dependent view of overlapping resonances coherent control.

<p> In an era of advancing printed electronics, solution-processable organic semiconductors continue to make significant strides in electronic and optoelectronic applications. Electrochromic (EC) technology, which encompass reversible optical modulation under electrochemical biasing, has progressed rapidly over the past half-century and developed into niche commercial-scale devices for auto-tinting glasses as well as low-power, non-emissive displays. To utilize the advantages of organic electrochromic materials in next-generation devices, it is imperative to understand their fundamental material properties, interactions with other device components, and the underlying electrochemistry that governs the overall optical and electrochemical response of the complete electrochromic device. This dissertation presents a discussion on the synergistic role of organic electrochromes, charge-balancing layers and electrolytes in determining two key performance metrics, namely the optical contrast and operational stability, of an electrochromic device (ECD). The absorption features of colored-to-transmissive switching conjugated polymers have been investigated by exploring material design strategies in conjunction with analytical approaches to optimize and enhance the optical contrast. In parallel, transmissive redox-active radical polymer counter electrodes have been developed as compatible charge-balancing layers and integrated into devices by pairing with electrochromic polymers (ECPs) to achieve stable and high-contrast optical modulation. Electrochemical activity of both conjugated and radical polymer electrodes in different ionic and solvent environments have been further examined to understand material-electrolyte interactions governing mixed ionic-electronic conduction. Finally, a small molecular approach to realizing transparent-to-colored electrochromism is discussed, where distinct substituent-induced degradation pathways of conjugated radical cations were revealed. Overall, this research aims to assist future development of robust, ultra-high contrast organic electrochromic platforms.  </p>

The critically important nature of radical and radical ion mechanisms in biology and chemistry continues to be recognized as our understanding of these unique transient species grows. The work presented herein demonstrates the versatility of kinetic studies for understanding the elementary chemical reactions of radicals and radical ions. Chapter 2 discusses the use of direct ultrafast kinetics techniques for investigation of crucially important enzymatic systems; while Chapter 3 demonstrates the value of indirect competition kinetics techniques for development of synthetic methodologies for commercially valuable classes of compounds. The mechanism of decay for aminyl radical cations has received considerable attention because of their suspected role as intermediates in the oxidation of tertiary amines by monoamine oxygenases and the cytochrome P450 family of enzymes. Radical cations are believed to undergo deprotonation as a key step in catalysis. KIE studies performed by previous researchers indicate N,N-dimethylaniline radical cations deprotonate in the presence of the bases acetate and pyridine. By studying the electrochemical kinetics of the reaction of para substituted N,N-dimethylaniline radical cations with acetate anion, we have produced compelling evidence to the contrary. Rather than deprotonation, acetate reacts with N,N-dimethylaniline radical cation by electron transfer, generating the neutral amine and acetoxyl radical. Transport properties of reactants and solvent polarity changes were investigated and confirmed not to influence the electrochemical behavior forming the basis for our mechanistic hypothesis. To reconcile our conclusion with earlier results, KIEs were reinvestigated electrochemically and by nanosecond laser flash photolysis. Rather than a primary isotope effect (associated with C-H bond cleavage), we believe the observed KIEs are secondary, and can be rationalized on the basis of a quantum effect due to hyperconjugative stabilization in aromatic radical cations during an electron transfer reaction. Product studies performed by constant potential coulometry indicate N,N-dimethylaniline radical cations are catalytic in carboxylate oxidations. Collectively, our results suggest that aminyl radical cation deprotonations may not be as facile as was previously thought, and that in some cases, may not occur at all. Interest in design and synthesis of selenium containing heterocycles stems from their ability to function as antioxidants, anti-virals, anti-inflammatories, and immunomodulators. To establish synthetic feasibility of intramolecular homolytic substitution at selenium for preparation of selenocycles, we set out to determine what factors influence cyclization kinetics. A series of photochemically labile Barton and Kim esters have been syntheisized and employed as radical precursors. The effect of leaving radical stability on kinetics has been investigated through determination of rate constants and activation parameters for intramolecular homolytic substitution of the corresponding radicals via competition experiments. Notable leaving group effects on measured kinetic parameters show more facile reactions for radical precursors with more stable leaving radicals. Moreover, cyclizations to form six-membered (as opposed to five- membered) ring systems exhibited order of magnitude decreases in rate constants for a given leaving radical. Our results are congruent with expectations for radical cyclizations trends for the varied experimental parameters and suggest homolytic substitution affords a convenient means for synthesis of selenocycles. / Ph. D.