Photodissociation methods have been explored for structural analysis of peptides and oligosaccharides. Ultraviolet photodissociation (UVPD) was applied to carboxylated derivatized peptides and reducing end derivatized oligosaccharides which offer selective dissociation and specific fragmentation pathways in comparison to CID. Upon UVPD of the modified peptides at carboxylate comprised of reduced y ions and increased immonium ions. The derivatized oligosaccharides via reductive amination and hydrazide conjugation can undergo highly efficient 355 nm UVPD and offer different fragmentation pathways. Both derivatization methods upon UVPD yielded [superscript 0,2] A-type ions, however reductive amination and hydrazide conjugation produced dominant [superscript 0,1] A and [superscript 2,4] A-type ions, respectively. Ultraviolet photodissociation at 193 nm (ArF laser, 6.4 eV / photon) has been applied to sialylated oligosaccharides and glycans which were analyzed in negative mode due to their acidic condition. Primarily, UVPD provides a greater array of fragment ions including cross-ring cleavages and dual cleavage internal ions in comparison to CID. In addition, the UVPD generates unique fragment ions which arise from site-specific cleavage of the trial substituent of the sialic acid residue. UVPD of doubly deprotonated sialylated oligosaccharides produced mostly singly deprotonated fragment ions, whereas the product ions in the CID spectra were overwhelmingly doubly charged ions, an outcome attributed to the more extensive cleavages of sialic acid residue upon UVPD. Although electron transfer dissociation (ETD) has shown superior capabilities for the characterization of post-translational modifications of peptides due to its non-eragodic property, ETD has intrinsic drawback arising from its significant dependence on the charge state of the selected precursor ion. Precursor ions in low charge states tend to undergo charge reduction, often preferentially relative to production of the informative cand z-type ions. In order to increase charge states of peptides and ETD efficiencies, peptides were derivatized at their carboxylate groups via attachment of amine with fixed charge or hydrophobic group. The carboxylate-derivatized peptides exhibited higher ETD efficiencies relative to underivatized peptides along with greater numbers of diagnostic fragment ions. The carboxylate derivatization strategy in combination with ETD for proteomics applications by the proteolytic digestion, the derivatization, and LC-MS purification was demonstrated with Cytochrome C.

Potential modulated attenuated total reflectance (PM-ATR) spectroscopy is a novel technique that makes it possible to sensitively monitor spectroscopic changes in an adsorbed molecular film as a function of applied potential. Here, PM-ATR was used to study charge transfer processes in Prussian blue (PB) and cytochrome c (cyt c) films deposited on indium tin oxide (ITO) electrodes.The electron transfer rate of PB films determined by PM-ATR was found to be in good agreement with the rate determined by conventional cyclic voltammetry, which validates the optical technique.The relationship between molecular orientation and electron transfer in adsorbed cyt c monolayers was investigated using PM-ATR. The electron transfer rate measured using TM polarized light was four-fold greater than that measured using TE polarized light. These data are the first to correlate a distribution of molecular orientations with a distribution of electron transfer rates in a redox-active molecular film.

In this research the environmental effects related to the position of a redox moiety with the electrochemical double layer were studied. This project was made possible with the synthesis of a series of lengths of ferrocene derived alkanethiols, a series of lengths of ferrocene derived norbornylogous bridges and a series of lengths of anthraquinone derived norbornylogous bridges. The series of ferrocene derived alkanethiols were used to study the effect of gradually varying the polarity of the self-assembled monolayers (SAMs) surface on the standard electron transfer rate constant and formal potential. This was achieved by varying the portion of hydroxyl to methyl terminated alkanethiol diluent in the SAM preparation step. It was found that the formal potential increased with a decreasing proportion of hydroxyl terminated diluent and increasing length of the diluent. For pure hydroxyl terminated diluent the formal potential was relatively independent of length. It was found that the rate constant increased for short alkane chain lengths with decreasing proportion of hydroxyl terminated diluent. However, it decreased in magnitude with long alkane chain lengths for low proportions of hydroxyl terminated diluent. The norbornylogous bridges were shown to stand proud above the diluent with a similar tilt angle as the alkanethiol diluent. The ferrocene derived norbornylogous bridges showed hydroxyl terminated monolayers had a slower rate constant then methyl terminated diluents independent of length and that it is highly probable that an alkane bridged redox moiety is located very close to the surface of the monolayer. SAMs were created with the ferrocene of the ferrocene derived norbornylogous bridges located at various heights above the monolayers surface. This was done by using various lengths of hydroxyl terminated diluent. It was found that the rate constant and the formal potential decreased with height above the surface. Interfacial potential distribution was used to account for this and to estimate a ??true?? formal potential. The anthraquinone derived norbornylogous bridges were tested at various pH values and heights above the surface. It was found that an accurate estimate for the electron transfer mechanism can not be made for surface bound species due to the effects of interfacial potential distribution. They demonstrated a novel technique for estimating the point of zero charge of the electrode.

Zugl.: Wien, Techn. University, Diss., 1997.

Orientador: Vitor Barbanti Pereira Leite / Banca: Fernando Luis Barroso da Silva / Banca: Luis Carlos Gomide de Freitas / Banca: Paulo César de Andrade / Banca: Elso Drigo Filho / Resumo: 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. / Abstract: 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. / Doutor

Dimethoxynaphthalene (donor) and quinone (acceptor) have been chosen as a suitable redox pair and are bonded to either permethylated silane chains or corresponding permethylated alkyl chains to form Acceptor-(Bridge)-Donor molecules. The idea that the s-delocalization phenomenon of silane chains may greatly facilitate ET reactions will be tested. The starting material for the donor precursor, 4-(1,4-dimethoxynaphthyl)bromocyclohexane, was 1,4-naphthoquinone. After methylation and bromination, the Grignard reagent of the resulting bromide was reacted with cyclohexanedione, mono ethylene ketal. The resulting alcohol was changed to the donor precursor through the following functional group transformation steps: dehydration, hydrogenation, deketalization and bromination. 1,4-Dibenzyloxybromobenzene, the precursor for the acceptor, was synthesized from 1,4-hydroquinone through bromination and benzylation. The connection of the two precursors and either permethylated silane chains or permethylated alkyl chains will give the final target molecules for ET research. Progress on this is included.

This dissertation demonstrates that it is possible to create a donor-acceptor system that can transform sunlight into electrons. By using site-directed synthesis, it was possible to create a novel trans-A2B2 porphyrin. In the pursuit of creating a supramolecular system, both the novel (TPA-BT)2ZnP and C60imidazole combined in solution such that the nitrogenous lone pair of C60 imidazole would coordinate axially to the zinc atom in the porphyrin. The conjugates' characterization utilized spectral, electrochemical, and computational techniques. Computational studies revealed in the optimized structure that the HOMO localized on the porphyrin and LUMO centered over the C60imidazole entity. Rehm-Weller calculations showed feasibility of singlet-electron transfer. Femtosecond transient absorption studies documented an efficient photoinduced charge separation in the conjugate. The subsequent work through steady-state and time-resolved transient absorption techniques that photoinduced electron transfer takes place between the synthesized phenylimidazole functionalized bisstyrylBODIPY (BDP(Im)2) and three selected zinc tetrapyrroles. This dyad consisted of BDP(Im)2 and either zinc tetratolylporphyrin (ZnP), zinc-tetra-t-butyl phthalocyanine (ZnPc), or zinc tetra-t-butyl naphthalocyanine (ZnNc) in a solution solvated by σ-dichlorobenzene (DCB). The three dyads (BDP(Im)2:ZnP, BDP(Im)2:ZnPc, and BDP(Im)2:ZnNc) were investigated by spectroscopic, computational, and electrochemical methods. The 1:1 complex of the dyads in optical absorption studies were approximately ~104 M-1 suggesting moderately stable binding. Spectral and electrochemical studies of the dyads used to generate energy level diagrams indicated that PET was thermodynamically unfavorable in BDP(Im)2:ZnP but favorable when the zinc tetrapyrrole is selectively excited dyads—as confirmed in femtosecond transient absorption studies. In the third work, two novel tetrads, consisting of charge stabilizing triphenylamine (TPA) to either bithiophene (BT) or terthiophene (TT) via a covalent linker that is attached to the meso-position of a BODIPY. This BODIPY was further extended by linking it to fulleropyrrolidine via a catechol linker to a modified BODIPY. Computational studies revealed the electronic structures of the tetrads, which rendered the HOMO to be on TPA-BT/TPA-TT moiety, while the HOMO-1 to be on the BODIPY entity and the LUMO to localized to the fulleropyrrolidine. Coupling the results with the electrochemistry, deduced that there is the formation of (TPA-TT).+-BODIPY-C60.- and (TPA-BT).+-BODIPY-C60.- as charge-separated states after the selective excitation of BODIPY in the tetrads. Femtosecond transient absorption studies were conducted in non-polar toluene and polar benzonitrile, and results affirmed photoinduced charge separation in the tetrads.

Two classes of trimetal nitride metallofullerenes, Sc3N@C n (n=68, 78) and MxSc3-xN@C80 (x=0-2), are investigated by Density Functional Theory with respect to their electronic properties and related geometric, energetic, and magnetic features. The substantial electron transfer from the metallic core to the fullerene cage makes these systems promising candidates for nonlinear optical devices. Pronounced magnetic effects associated with complexes that enclose lanthanide constituents suggest their suitability as contrast agents in biomedical imaging.

Nitrogen is a critical nutrient for growth and reproduction in living organisms. Although the Earth’s atmosphere is composed of ~80% nitrogen gas (N2), it is inaccessible to most living organisms in that form. Biological nitrogen fixation, however, can be performed by microbes that harbor the enzyme nitrogenase. This enzyme converts N2 into bioavailable ammonia (NH3) and accounts for at least half of the “fixed”nitrogen on the planet. The other major contributor to ammonia production is the industrial Haber-Bosch process. While the Haber-Bosch process has made significant advances in sustaining the global food supply through the generation of fertilizer, it requires high temperature and pressure and fossil fuels. This makes nitrogenase an ideal system for study, as it is capable of performing this challenging chemistry under ambient conditions and without fossil fuels. Nitrogenase requires energy and electrons to convert N2into NH3. The work presented here examined how the enzyme receives electrons to perform the reaction. It was discovered that some microbes employ a novel mechanism that adjusts the energy state of the electrons so that nitrogenase can accept them. Further, the slowest step that takes place in nitrogenase once the electrons are taken up was identified. Finally, by capitalizing on fundamental knowledge, a biohybrid system was designed to grow nitrogen-fixing bacteria in association with electrodes for light-driven production of fixed nitrogen that has potential to be used as a fertilizer for plant growth. Gaining an in-depth understanding of nitrogenase provides insight into one of the most challenging biological reactions, and the newfound knowledge may be a catalyst in developing more efficient systems for sustainable ammonia production.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20426号 / 農博第2211号 / 新制||農||1048(附属図書館) / 学位論文||H29||N5047(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 加納 健司, 教授 植田 充美, 教授 三上 文三 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM