Fluorescent molecules commonly shift to transient dark states, induced bylight or triggered by chemical reactions. The transient dark states can beused as probes of the local environment surrounding the fluorescent molecules,and are therefore attractive for use in biomolecular applications. Thisthesis explores the use and development of novel fluorescence spectroscopictechniques for monitoring transient dark states.This work demonstrates that kinetic information regarding photoinduced transient dark states of fluorescent molecules can be obtained from the time-averaged fluorescence intensity of fluorescent molecules subject totemporally modulated illumination. Methods based on this approach havethe advantage that the light detectors can have a low time resolution, which allows for parallelization and screening of biomolecular interactions withhigh throughput. Transient state images are presented displaying local environmental differences such as those in oxygen concentration and quencher accessibility.Analysis of the fluorescence intensity fluctuations resulting from thetransitions to and from transient dark states can be used to obtain information regarding the transition rates and occupancy of the transient darkstates. Fluorescence fluctuation analysis was used to reveal rates of protonbinding and debinding to single fluorescent molecules located close to biological membranes and protein surfaces. The results from these studies show that the proton exchange rate increases dramatically when the fluorescent molecule is close to the membrane. / QC 20100809

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 164-177).

Heme-copper oxidases are transmembrane proteins that are found in aerobic and anaerobic respiratory chains. During aerobic respiration, these enzymes reduce dioxygen to water. The energy released in the reaction is used to transport protons across a biological membrane. Stored as proton electrochemical gradient, the energy can be used to regenerate ATP. It is known that aa3 oxidases, which are the most common oxidases, transport pumped protons and protons used for the catalytic reaction using two proton pathways. However, the molecular mechanism of pumping is still being debated. When oxygen is available in very small quantities, oxygen reductases with high affinity for oxygen are expressed by organisms like Thermus thermophilus. The proton pumping mechanism in the ba3 oxidase is slightly different from that of aa3 oxidases as this enzyme only uses a single proton uptake pathway. Here we analyzed the reaction mechanism of ba3 oxidase and found evidence that the first proton taken up by the four-electron reduced ba3 oxidase is transferred to a site distant from the catalytic site, the pump site, and that only every second proton taken up from solution is pumped. Data obtained from studies using site-directed mutagenesis and flow-flash spectroscopy suggest a probable location of the pump site. Under anaerobic conditions, some organisms are able to generate a proton- motive force using nitrate and nitrite as electron acceptors. In this process, the cytotoxic reaction intermediate nitric oxide is produced. Nitric oxide reductase (NOR), a deviant heme-copper oxidase that reduces NO to the rather harmless N2O, does not pump any protons. The catalytic mechanism of nitric oxide reduction by NOR is very poorly understood. Here we demonstrate that substrate inhibition, which occurs in NOR from Paracoccus denitrificans above 5 μM NO, can already be observed before the electrons from the low-spin hemes re-distribute to the active site. Furthermore, we found that a single specific proton pathway is used for proton-transfer leading from the periplasm to the active site.

London or dispersion interactions are weak van der Waals (vdW) interactions. They are important in determining the structure and properties of many chemical and biochemical systems. In this thesis, an optimizer using the nonempirical generalized gradient approximation (GGA) functional PW86+PBE+XDM, to capture van der Waals interactions, is presented. The work in this thesis covers the assessment of a variety of basis sets for their ability to reproduce accurate GGA repulsive and binding energies. Selected basis sets were then used to compute binding energies of 65 vdW complexes at equilibrium. This functional was also tested for binding energies of two sets of vdW complexes at distorted geometries. The last part deals with forces to investigate their accuracy using PW86+PBE+XDM in order to build an optimizer for vdW complexes using a nonempirical DFT method. Eventually, after confirming a high reproducibility of the optimizer on the geometries and binding energies, it was used in two biologically relevant applications. This optimizer is a unique tool to compute deformation energies with a nonempirical DFT method. The second part of this thesis covers a biologically relevant application where a conventional DFT is used. This application is related to the carrier of the genetic codes in living cells, DNA. DNA undergoes harmful mutations under external perturbations such as applied external electric fields. In this study, DNA base pairs were first mimicked by a simpler model, namely, the formic acid dimer. The effect of applied external electric fields on the geometries of the formic acid dimer is studied. The effect of these applied fields on the potential energy surface, the barrier height and the frequency of the double proton transfer in the formic acid dimer are also investigated. The study was then repeated on DNA base pairs to study the effect of an external applied electric field on the tunneling corrected rate constants of the double proton transfer reactions in AT and GC.

A detailed understanding of natural photosynthesis provides inspiration for the development of sustainable and renewable energy sources, i.e. a technology that is capable of converting solar energy directly into chemical fuels. This concept is called artificial photosynthesis. The work described in this thesis contains contributions to the development of artificial photosynthesis in two separate areas. The first one relates to light harvesting with a focus on the question of how electronic properties of photosensitizers can be tuned to allow for efficient photo-induced electron transfer processes. The study is based on a series of bis(tridentate)ruthenium(II) polypyridyl complexes, the geometric properties of which make them highly appealing for the construction of linear donor-photosensitizer-acceptor arrangements for efficient vectorial photo-induced electron transfer reactions. The chromophores possess remarkably long lived 3MLCT excited states and it is shown that their excited-state oxidation strength can be altered by variations of the ligand scaffold over a remarkably large range of 900 mV. The second area of relevance to natural and artificial photosynthesis that is discussed in this thesis relates to the coupled movement of protons and electrons. The delicate interplay between these two charged particles regulates thermodynamic and kinetic aspects in many key elementary steps of natural photosynthesis, and further studies are needed to fully understand this concept. The studies are based on redox active phenols with intramolecular hydrogen bonds to quinolines. The compounds thus bear a strong resemblance to the tyrosine/histidine couple in photosystem II, i.e. the water-plastoquinone oxidoreductase enzyme in photosynthesis. The design of the biomimetic models is such that the distance between the proton donor and acceptor is varied, enabling studies on the effect the proton transfer distance has on the rate of proton-coupled electron transfer reactions. The results of the studies have implications for the development of artificial photosynthesis, in particular in connection with redox leveling, charge accumulation, as well as electron and proton transfer. In addition to these two contributions, the excited-state dynamics of the intramolecular hydrogen-bonded phenols was investigated, thereby revealing design principles for technological applications based on excited-state intramolecular proton transfer and photoinduced tautomerization.

This Thesis aims to examine the effects of substituents on the adjacent proton accepting phenyl ring with respect to a new type of excited state intramolecular proton transfer (ESIPT) process discovered by Wan and co-workers. Therefore, a number of 2-phenylphenols 23-28 were synthesized with electron-donor and electron-acceptor substituents such as methyl, methoxy, and ketone moieties on the adjacent proton accepting phenyl ring. The results obtained from examination of photochemical deuterium exchange showed that all derivatives except for ketone 27 underwent deuterium exchange (Фex = 0.019 - 0.079), primarily at the 2’-position on photolysis in D2O-CH3CN. In general, compounds with methoxy moiety (ies) on the adjacent proton accepting ring showed higher deuterium exchange yields. Diol 28 has the potential to undergo photosolvolysis as well as ESIPT process since it has both a benzyl alcohol and a phenol chromophore on the same molecule. Irradiation of 28 in 1:1 H2O-CH3OH gave the corresponding methyl ether product in high yield. Photolysis of 28 in 1:1 D2O-CH3OH also showed that ESIPT competes very well with photosolvolysis. Thus, this work has established that ESIPT can compete efficiently with photosolvolysis. Semi-empirical AM1 (examination of HOMOs and LUMOs) calculations show a large degree of charge transfer in the electronic excited state (except 27), from the phenol ring to the attached phenyl ring of the studied compounds. The AM1 calculation for ketone 27 showed that the carbonyl oxygen is more basic than the carbon atoms of the benzene ring, which explains the lack of deuterium exchange observed for 27.

Photosystem II (PSII) is the membrane-bound oxidoreductase peptide complex responsible for the oxidation of water to molecular oxygen and reduction of plastoquinone to plastoquinol. Primary electron transfer is initiated upon absorption of a photon by the primary donor chl resulting in electron transfer and production of a P680+QA charge separated state. P680+ is reduced by YZ (Y161 of the D1 polypeptide subunit), one of two redox-active tyrosine residues found in PSII. This produces a neutral tyrosyl radical (YZ ) which is subsequently reduced by electrons derived from water at the oxygen-evolving complex (OEC). The OEC is composed of four manganese, one calcium ion, and one chloride ion. Four photons are required to convert water to O2, each photon advancing the OEC through successive oxidation states or S states. The exact chemical mechanism of water oxidation in PSII is not known. However, proton-coupled electron transfer (PCET) is thought to be one of the fundamental steps in driving the extraction of electrons and protons from water. Here, the mechanism of water oxidation is investigated with focus on PCET events using vibrational spectroscopy. Vibrational spectroscopy is sensitive to changes in protein structure, charge, and hydrogen bonding, and is ideal for the study of fast events coupled with light-induced electron transfer. The results presented here demonstrate the utility of time-resolved infrared spectroscopy in the detection of intermediates of photosynthetic water oxidation. We suggest that proton transfer may precede manganese oxidation during water oxidation based on time-resolved infrared and difference FT-IR spectroscopic results. The mechanism of PCET associated with YZ reduction is investigated. Using reaction-induced difference FT-IR spectroscopy, the identity of the chloride binding site is speculated through the use of bromide exchange at the OEC. Also, proton transfer reactions at the OEC are investigated using azide as a vibrational probe. The advances in the understanding of photosynthetic water oxidation gained in this work will aid in the elucidation of the chemical mechanism of this important reaction. Understanding the details of photosynthetic water oxidation will assist in the development of technology aimed at harnessing the energy of the sun for the benefit of humankind.

Thesis (Ph. D.)--Ohio State University, 2005. / Title from first page of PDF file. Includes bibliographical references (p. 164-174).

La synthèse de l'adénosine triphosphate (ATP) est un événement clé dans la bioénergétique cellulaire. ATP synthesis est possible quand un gradient de potentiel électrochimique de protons est présent sur les membranes des cellules ou des organelles. Ce gradient est produit par les réactions d'oxydoréduction ou les réactions photochimiques qui sont contrôlées par l'enzyme. Bactériorhodopsine (bR) est la protéine la plus simple et la plus étudiée qui convertit l'énergie lumineuse en potentiel électrochimique. bR est un protéine transmembranaire de Halobacterium salinarum. bR absorbe des photons de lumière et transmet un proton à partir du cytoplasme vers l'espace extracellulaire. Grâce à sa disponibilité en relativement grandes quantités, la procédure de purification facile et stable, bR reste un des protéines membranaire les plus étudiés au cours des 40 dernières années.Pour comprendre le mécanisme moléculaire de la bR fonctionnement il faut connaître les changements structurels, provoqués par l'absorption de photon, qui accompagnent le cycle de travail des protéines et poussent à transporter le proton. Cela implique l'obtention des structures cristallographiques de bR état fonctionnel avec une résolution atomique. Selon cette approche, il est important d'avoir les cristaux protéiques très ordonnés et les méthodes de fixage des molécules de protéines dans les états intermédiaires. Les méthodes de fixage dans des conditions cryogéniques ont été développées précédemment. Les cristaux de la qualité désirée peuvent être obtenus par la cristallisation in meso où lipide mésophase bicontinue est utilisé pour la cristallisation des protéines membranaires.Le mécanisme de la cristallisation in meso est actuellement étudié pauvrement. Cette situation limite grandement son application potentielle pour des protéines membranaires. Malgré ses limites l’approche in meso a récemment permis d'obtenir les structures de base ainsi que les structures intermédiaires des états de bR. Cependant, différents groupes de scientifiques ont publié de différents structures cristallographiques des mêmes états intermédiaires. Les mécanismes de protons transport proposés par des auteurs différents sont contradictoires. Les raisons de l'absence de consensus dans les structures intermédiaires restent floues. Les raisons possibles discutées dans la littérature sont: la qualité insuffisante de la diffraction des cristaux protéiques, twinning merohedral et détérioration des cristaux par l'irradiation de rayonnement X, ainsi que la génération de nouvelles protéines états provoqués par rayons X.L'objectif de l'étude était de trier les raisons de contradictions dans le domaine de l'analyse cristallographique de bR états fonctionnels et de trouver des moyens de surmonter les problèmes connexes. Ceci implique plusieurs sous-objectifs distincts: l'étude de twinning merohedral de bR cristaux; étude des changements dans la structure bR induit par les 'irradiation de rayonnement X; étude des changements structurels dans bR par les petites doses de radiations. Un autre objectif de ce travail était d'étudier un rôle de molécules de la matrice de in meso cristallisation dans la stabilisation des cristaux de protéines membranaires. / The synthesis of adenosine triphosphate (ATP) is a key event in the cell bioenergetics. ATP synthesis is only possible when a proton electrochemical potential gradient is present on the membranes of cell or organelle. This gradient is produced by enzyme-controlled redox or photochemical reactions. Bacteriorhodopsin (bR) is the simplest and most studied protein that converts light energy into electrochemical potential. Being transmembrane protein of Halobacterium salinarum it absorbs light photon and transfers a proton from the cytoplasmic to the extracellular space. Due to its availability of relatively large quantities, easy purification procedure and protein stability bR remains one of the most extensively studied membrane proteins during the past 40 years.Current state of investigated problems. To understand the molecular mechanism of bR functioning is necessary to know the structural changes caused by light absorption which accompany the protein working cycle and lead to the directional transport of the proton. It implies obtaining of X-ray structures of bR functional states with atomic resolution. Following this approach it is important to have highly ordered three-dimensional protein crystals on the one hand and effective methods of trapping protein molecules in intermediate states on the other one. Trapping procedures for bR intermediate states under cryogenic conditions have been developed previously. Crystals of the desired quality can be obtained by in meso crystallization where lipid bicontinuous mesophase is used for the crystallization of membrane proteins. The mechanism of in meso crystallization is currently poorly investigated. This situation greatly limits its potential applicability for membrane proteins. Despite its limitations in meso approach have recently made possible to obtain the ground and some intermediate states structures of bR. However, different scientific groups have published different X-ray models of the same bR intermediate states. The proposed by different authors mechanisms of proton transport are contradictory. The reasons for the lack of the consensus in intermediate structures remain unclear. The possible reasons for this contradiction which have been discussed in literature are: insufficient quality of diffraction data, merohedral twinning and radiation damage of protein crystals, as well as the generation of new protein states caused by X-ray illumination.The aim of the study was to sort out the reasons for contradictions in the field of X-ray crystallographic analysis of bR functional states and to find ways to overcome related problems. This implies several separate subgoals: study of merohedral twinning of bR crystals; study of X-ray-radiation-induced changes in bR structure; study of low-dose radiation-induced structural changes in bR structure. An additional goal of the work was to study a role of molecules of the in meso crystallization matrix in the stabilization of membrane protein crystals.

As antocianinas compreendem o maior conjunto de pigmentos solúveis em água do reino vegetal. A absorção da luz por estes compostos, responsáveis pelas cores vermelha, azul e roxa da maioria das frutas e flores, é produto de combinações de vários fatores, como o número de substituintes, a presença ou não de outras moléculas capazes de estabilizar a cor (“co-pigmentos”), o pH local do meio e a natureza do microambiente em que a antocianina se encontra. A reatividade química e fotoquímica das antocianinas já é relativamente complexa em solução aquosa na ausência de micelas, onde cada um dos processos químicos e fotoquímicos ocorre numa faixa de tempo distinta. Uma forma de se diminuir o número de espécies em solução é o emprego de antocianinas sintéticas com estruturas simplificadas, conhecidas como sais de flavílio, cuja variação no número, posição e tipo químico de substituinte permite um certo controle sobre as frações molares das espécies. Neste estudo procurou-se compreender os processos que regem o equilíbrio ácido-base e a hidratação do cátion flavílio em ambiente micelar. Estes dois processos exercem um papel central na estabilização da cor em antocianinas. Foram utilizados três sais de flavílio: o 4-carboxi-7-hidroxi-4\'-metoxiflavílio (CHMF), o 2-fenilbenzopirílio e o 4\'-metoxiflavílio. Os dois grupos ionizáveis do CHMF possuem pKas distintos (pKa1 = 0,73; pKa2 = 4,84), cujas dinâmicas de protonação/desprotonação são influenciadas pelas micelas de SDS de modos diferentes. O cátion é estabilizado preferencialmente pelas micelas aniônicas em relação ao zwitterion (pKa1SDS = 2,77), que por sua vez é mais favorecido que a base quinonoidal (pKa2SDS = 5,64). A estabilização do cátion está relacionada com as fortes interações eletrostáticas entre a espécie e a micela carregada negativamente. A base quinonoidal, que no caso específico do CHMF tem carga negativa, é desfavorecida em relação ao zwitterion. Adicionalmente, em SDS praticamente não se observa hidrólise da espécie zwitteriônica. Com relação ao 2-fenilbenzopirílio (pKw = 3,01) e o 4\'-metoxiflavílio (pKw = 4,47), a primeira observação feita é que a inclusão do grupo metoxi na posição C4\' estabiliza o cátion flavílio, diminuindo a extensão da hidrólise por meio de transferência de carga para o anel central. O efeito de estabilização do cátion pelo ambiente micelar, verificado pelo aumento do pKw, é mais pronunciado no 2-fenilbenzopirílio (pKwSDS = 4,73) do que no 4\'-metoxiflavílio (pKwSDS = 5,05). Os processos cinéticos mostram que a reação de hidratação (kw) do flavílio sem substituintes diminui 65 vezes em SDS, enquanto que a reação no sentido inverso se mantém dentro da mesma ordem de magnitude. Já no caso do 4\'-metoxiflavílio, foi verificado que ambas as constantes de velocidade aumentam, mas a constante de desidratação do hemicetal (k-w), que depende da concentração de prótons, é a mais afetada, aumentando cerca de 15 vezes. Este fato é um indicativo de que o pH na interface micelar é o fator de estabilização do cátion do 4\'-metoxiflavílio. Adicionalmente foram feitos cálculos computacionais de transições eletrônicas, pKa e potenciais de redução em nível ab initio para um conjunto cátions flavílios e respectivas bases quinonoidais. Os valores de pKa calculados apresentaram um desvio médio de +/- 0,5 unidade de pKa. / Anthocyanins comprise the major water-soluble pigment group in the Plant Kingdom. Light absorption by these compounds is responsible for the diverse colors in many flowers and fruits and can be modulated by phenomena such as self-association of flavylium cations or anhydrobases, copigmentation with other polyphenols and flavonoids, complexation with metal ions, incorporation of anthocyanins into microaggregates like micelles and the pH of the medium. The chemical and photochemical reactivity of anthocyanins is quite complex in aqueous solution and each process occurs in a different time range. The use of structurally simplified synthetic flavylium salts permits a certain control over the mole fractions of the various species in solution. In this study we used the synthetic flavylium ions 4-carboxy-7-hydroxy-4\'-methoxyflavylium (CHMF), 2-phenylbenzopyrylium and 4´-methoxyflavylium to investigate the main processes that influence the acid-base equilibrium and hydration of the flavylium cation in micellar environments. Such reactions play a central role in color stabilization of anthocyanins. CHMF has two ionizable groups with distinct pKas (pKa1 = 0,73; pKa2 = 4,84), and the protonation/deprotonation dynamics of these groups are affected differently by SDS micelles. The results show that SDS micelles stabilize the cationic form rather than the zwitterion (pKa1SDS = 2,77), which is favored relative to the quinonoidal base (pKa2SDS = 5,64). The preferential stabilization of the cation is related to electrostatic interactions of this form with the anionic micelle. The quinonoidal base, which in the specific case of CHMF is an anion, is disfavored relative to the zwitterion. In addition, the hydrolysis of the zwitterionic form is substantially reduced in micellar SDS solutions. The comparison of 2-phenylbenzopyrylium (pKw = 3,01) and 4´-methoxyflavylium (pKw = 4,47) shows that the methoxy group at the C4´ position stabilizes the cationic form, reducing the hydration by charge transfer to the central ring. The stabilization of the cationic form by the micellar environment, which is reflected in the increase of the pKw, is more pronounced for the 2-phenylbenzopyrylium cation (pKwSDS = 4,73) than for 4´-methoxyflavylium (pKwSDS = 5,05). Kinetic studies of the 2-phenylbenzopyrylium ion in SDS indicate a 65-fold reduction in the hydration rate constant (kw), while the inverse reaction has the same magnitude as in water. In the case of the 4´-methoxyflavylium ion, both rate constants associated with the equilibrium between the flavylium cation and hemicetal increased. However, the [H+]-dependent rate constant for dehydration of the hemicetal is affected to a greater extent, increasing about 15 fold, indicating stabilization of the 4\'-methoxyflavylium cation by the micellar interface. Finally, computational calculations were performed at the ab initio level for several flavylium cations and anhydrobases to estimate the electronic transitions, pKa and reduction potentials. The quality of the calculated pKa results were compared with experimental data and the mean absolute deviation is +/- 0.5 pKa unit.