Dissertations / Theses: 'Proton transfer reactions'

1

Redondo, Marey Carmen-Maria. "Femtodynamics of double proton transfer reactions." Thesis, University College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.398981.

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2

Linares-Samaniego, Sandra I. "Excited state proton transfer in microheterogeneous conditions." Diss., Georgia Institute of Technology, 1997. http://hdl.handle.net/1853/27263.

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3

Papageorgiou, Alexia. "Influence of proton transfer kinetics and natural convection on Proton-Coupled Electron Transfer (PCET) reactions." Doctoral thesis, Universite Libre de Bruxelles, 2021. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/318308.

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Les phénomènes de transport de matière ainsi que la cinétique des réactions chimiques sont des processus importants en électrochimie car ceux-ci contrôlent le courant mesuré. Dans ce contexte, nous nous intéressons à de simples réactions électrochimiques et à la classe des réactions de transfert couplés électrons-protons (PCET), jouant un rôle important dans les phénomènes biologiques et la conversion d’énergie. Ces réactions impliquent le transfert d’électron(s) et de proton(s) et sont représentées par un schéma carré. Alors que la cinétique de transfert d’électrons est largement étudiée, la cinétique de transfert de protons l’est plus rarement. Ces réactions sont en effet supposées être très rapides alors qu’il existe des situations où les réactions de protonation constituent l’étape limitante. La première partie de la thèse consiste à étudier la cinétique des réactions de protonation en tenant compte de la catalyse de Brönsted. Par le biais de simulations numériques, nous montrons que la catalyse augmente la réversibilité des voltampérogrammes cycliques, à des pH où le transfert couplé s’opère. Les prédictions numériques ont été comparées aux données expérimentales et les résultats sont encourageants car une même tendance est observée. L’accord quantitatif n’est cependant pas satisfaisant à ce stade. Les phénomènes de transport étant connus pour affecter les processus à l’électrode, la seconde partie de la thèse est consacrée à l’étude de l’influence de la convection. Nous commençons par présenter les différentes raisons qui peuvent expliquer les déviations expérimentales par rapport à la diffusion seule, comme la convection naturelle induite par des gradients de densité ou de tension superficielle. Nous présentons le concept de convection spontanée associé aux mouvements microscopiques de la solution. Bien que les fondements théoriques de la convection spontanée soient discutables, la théorie permet de reproduire les résultats d’un certain nombre d’expériences, souvent pratiquées en conditions non contrôlées. Ensuite, nous évaluons l’influence de la convection naturelle sur de simples réactions électrochimiques, avant de passer à l’étude des réactions PCET. Les simulations numériques nous ont permis de prévoir la déviation des chronoampérogrammes par rapport à une situation diffusive en fonction de la durée de l’expérience et de la contribution de chaque espèce à la densité de la solution. Pour une électrode située au bord supérieur, la production d’espèces plus denses amène une déviation du courant plus importante, dû au développement d’instabilités hydrodynamiques. La convection due aux gradients de densité est supposée être accentuée lorsque que les réactions électrochimiques sont couplées avec des réactions chimiques, ce qui est la définition même des PCET. Cependant, nous avons conclu à un impact négligeable de celles-ci, sauf pour de faibles valeurs de constantes cinétiques. Pour conclure, nous avons évalué d’une part l’impact de la convection due aux effets Marangoni et d’autre part son couplage à la convection induite par des gradients de densité. L’influence de ces mouvements convectifs sur le courant résultant dépend des propriétés des réactifs et des produits de la réaction, mais également de la présence d’une surface libre.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

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4

Cooper, Ian Blake. "Photosynthetic water oxidation and proton-coupled electron transfer." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26707.

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Thesis (Ph. D.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009.
Committee Chair: Bridgette Barry; Committee Member: El-Sayed, Mostafa; Committee Member: Fahrni, Christoph; Committee Member: Kröger, Nils; Committee Member: McCarty, Nael. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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5

Fernandez, M. T. N. "Thermodynamics of proton transfer reactions in the gas phase." Thesis, University of Warwick, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.378296.

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6

Jenson, David L. Jenson. "Proton-coupled electron transfer and tyrosine D of phototsystem II." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/29667.

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Thesis (Ph. D.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2010.
Committee Chair: Bridgette Barry; Committee Member: Ingeborg Schmidt-Krey; Committee Member: Jake Soper; Committee Member: Nils Kroger; Committee Member: Wendy Kelly. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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7

Maza, William Antonio. "Reaction Enthalpy and Volume Profiles for Excited State Reactions Involving Electron Transfer and Proton-Coupled Electron Transfer." Scholar Commons, 2013. http://scholarcommons.usf.edu/etd/4539.

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Electron transfer, ET, and proton-coupled electron transfer, PCET, reactions are central to biological reactions involving catalysis, energy conversion and energy storage. The movement of electrons and protons in either a sequential or concerted manner are coupled in a series of elementary reaction steps in respiration and photosynthesis to harvest and convert energy consumed in foodstuffs or by absorption of light into high energy chemi-cal bonds in the form of ATP. These electron transfer processes may be modulated by conformational dynamics within the protein matrix or at the protein-protein interface, the energetics of which are still not well understood. Photoacoustic calorimetry is an estab-lished method of obtaining time-resolved reaction enthalpy and volume changes on the nanosecond to microsecond timescale. Photoacoustic calorimetry is used here to probe 1) the energetics and volume changes for ET between the self-assembled anionic uroporphy-rin:cytochrome c complex and the role of the observed volume changes in modulating ET within the complex, 2) the enthalpy and volume change for the excited state PCET reac-tion of a tyramine functionalized ruthenium(II) bis-(2,2'-bipyridine)(4-carboxy-4'-methyl-2,2'-bipyrine) meant to be a model for the tyrosine PCET chemistry carried out by cyto-chrome c oxidase and photosystem II, 3) the enthalpy and volume changes related to car-bon monoxide and tryptophan migration in heme tryptophan catabolic enzyme indoleam-ine 2,3-dioxygenase.

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8

Murphy, Christine Fecenko Thorp H. Holden. "Coupled electron proton transfer reactions in biological redox active substrates." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2009. http://dc.lib.unc.edu/u?/etd,2895.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2010.
Title from electronic title page (viewed Jun. 23, 2010). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.

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9

Marks, David Roland Azoulai. "Femtosecond studies of excited-state proton transfer reactions in solutions." [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2000. http://dare.uva.nl/document/82013.

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10

Meng, Kejie. "MECHANISTIC STUDIES OF PROTON-COUPLED ELECTRON TRANSFER REACTIONS INVOLVING ANTIOXIDANTS." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5498.

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The objective of the research was to investigate proton-coupled electron transfer (PCET) reactions involving antioxidants to gain insight into the detailed mechanisms of glutathione (GSH), Trolox, and α-tocopherol (α-TOH). PCET reactions are complex redox reactions that transfer electrons and protons sequentially or in concert. These reactions are ubiquitous in natural or artificial processes that produce electrochemical energy that is extractable as electricity or as chemical fuels of high energy content. Examples of processes based on PCET are photosynthesis, respiration, nitrogen fixation, carbon dioxide reduction, redox fuel cells, and artificial photosynthesis. Antioxidants were selected as a PCET model to understand the coupling between proton transfer (PT) and electron transfer (ET) in order to elucidate structure-reactivity relationships under different experimental conditions. PCET reactions were studied with a set of electrochemical techniques to propose a preliminary mechanism that could be validated with digital simulations matching the electrochemical response. In some cases, other analytical techniques were used to aid in the system characterization. This thesis presents the results and discussion of the effects of oxidant-base pairs on the mediated oxidation of GSH, the -2e-/-H+ process of Trolox in aqueous and nonaqueous solvents with various pH values, and the particle collision electrolysis of α-tocopherol in oil-in-water emulsion droplets on an ultramicroelectrode. Ultimately our goal was to determine the kinetic and thermodynamic factors that control PCET reactions so that they can be applied in designing artificial systems for the production of energy using more abundant reagents with lower cost and better yields.

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Sullivan, Erica N. "Photoexcited hydroxyarenes as probes for microenvironments." Diss., Georgia Institute of Technology, 2000. http://hdl.handle.net/1853/27440.

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12

Harvey, Lilia Cuesta. "Excited state proton transfer in ortho substituted naphthols : Part II Mechanistic studies of ortho allyl-naphthol photocyclizations." Diss., Georgia Institute of Technology, 1992. http://hdl.handle.net/1853/30017.

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13

Wan, Min. "1,3 proton transfer catalysts supported by Merrifield resin or Jeffamine gel." Scholarly Commons, 1998. https://scholarlycommons.pacific.edu/uop_etds/2344.

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6-Chloronicotinic acid was coupled by an amide linkage to Merrifield resin or Jeffamine gel. Nucleophilic displacement of the 6-chloride group by hydroxide gave novel Merrifield resin catalyst 6 or Jeffamine gel catalyst 9 that were successfully used for Henry condensations. The condensation of 4,6-O-benzylidene-β-D-glucopyranose 11 with nitromethane gave 4,6-O-benzylidene-D-glucopyranosyl-l-nitromethane 12; the condensation of 11 with nitroethane gave α-R-(4,6-O-benzylidene-β-D-glucopyranosyl)-1-nitroethane 13 and its diastereomer 15; the condensation of 11 with nitropropane, followed by acetylation, gave α-R-(2,3-di-O-acetyl-4,6-O-benzylidene-β- D-glucopyranosyl)-1 -nitropropane 16 and its diastereomer 17; the condensation of 4,6- O-isopropylidene-β-D-glucopyranose 19 with nitromethane gave 4,6-O-isopropylidene- β-D-glucopyranosyl-1-nitromethane 20; the condensation of 4,6-O-isopropylidene-α- D-mannopyranose 21 with nitromethane gave 4,6-O-isopropylidene-β-D-mannopyranosyl- 1-nitromethane 23. These known compounds were obtained with improved yields compared to protocols with 1,3 proton transfer catalysts that were not bound to polymers. A new monomeric 1,3 proton transfer catalyst, 2,4 (1,3)-quinazolinedione 10, was also introduced.

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14

Beelen, Eric Stephan Edmond van. "Proton transfer and ligand exchange induced reactions in the gas phase." [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2005. http://dare.uva.nl/document/18421.

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15

Patel, Jagvi Ramesh. "Kinetics and mechanism of hydrolysis and proton transfer reactions in solution." Thesis, King's College London (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.271412.

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16

Adekola, Aderemi S. "Proton-transfer study of unbound ¹⁹Ne states via ²H(¹⁸F,[alpha]¹⁵O)n REACTION." Ohio : Ohio University, 2009. http://www.ohiolink.edu/etd/view.cgi?ohiou1230079038.

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17

Liu, Ping. "Composite proton exchange membranes for fuel cells." Diss., Connect to online resource - MSU authorized users, 2006.

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18

Ädelroth, Pia. "Mechanisms and pathways for proton transfer in cytochrome-c oxidase." Göteborg : Göteborg University, 1998. http://catalog.hathitrust.org/api/volumes/oclc/68945135.html.

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19

Choi, Pyoungho. "Investigation of thermodynamic and transport properties of proton-exchange membranes in fuel cell applications." Link to electronic thesis, 2004. http://www.wpi.edu/Pubs/ETD/Available/etd-0430104-094215/.

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20

Xu, Shujuan. "EPR studies of electron and proton transfer in cytochrome c oxidase." Diss., Connect to online resource - MSU authorized users, 2008.

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Thesis (Ph. D.)--Michigan State University. Chemistry, Biochemistry and Molecular Biology, 2008.
Title from PDF t.p. (viewed on July 2, 2009) Includes bibliographical references. Also issued in print.

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21

Wyngaardt, Shaun Metzler. "Relativistic plane wave description of spin transfer observables for proton knockout reactions." Thesis, Stellenbosch : Stellenbosch University, 2001. http://hdl.handle.net/10019.1/52429.

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Thesis (PhD)--Stellenbosch University, 2001.
ENGLISH ABSTRACT: In this dissertation we set out to develop the first relativistic model for calculating complete sets of (p, 2p) spin transfer observables. In addition to this a new technique has been developed which allows us to evaluate the transition amplitude, which is used to calculate the scattering observables for the reaction directly. The influence of various modiuin-modificd parameters ()1I the scattered wave functions anr] NN interact ion lH-IVC' })('('11 invest igatcd DlIC t,C) (I,llIlJigllitic's surrounding the nNN coupling we have included both pseudosoalar and pseudovector coupling into the nucleon-nucleon interaction model. Furthermore we have included two different kinematic prescriptions to obtain the effective NN laboratory kinetic energy and center of mass scattering angle, which are used to obtain the NN scattering amplitudes. The aim of this study is to investigate the effects of the various model parameters on complete sets of scattering observables. Our investigation has shown that although the analyzing power is not very sensitive to nuclear medium effects, and the various other spin transfer observables such as Dnn should provide valuable insight. Further refinements of the model would be to include nuclear distortions as well as the IA2 model of the NN interaction.
AFRIKAANSE OPSOMMING: In hierdie tesis ontwikkel ons die eerste relatiwistiese model vir die berekening van 'n volledige stel (p, 2p) spin waarneembares. Verder word 'n nuwe tegniek ingevoer wat ons toelaat om die oorgangsamplitude, wat gebruik word in berekening van die verstrooings waarneembares vir die reaksie, direk te evalueer. Die invloed van verskeie medium-gemodifiseerde parameters op die verstrooide golffunksies en die NN wisselwerking word bestudeer. As gevolg van onsekerhede betreffende die лNN koppeling word beide die pseudoskalaar en pseudovektor koppeling in die nukleon-nukleon interaksie model ingesluit. Ons sluit ook twee verskillende kinematiese preskripsies in om die effektiewe NN laboratorium kinetiese energie en die massa middelpunt verstrooiings hoek, wat gebruik word vir die berekening van die NN verstrooiings amplitude, te bereken. Die doel van hierdie studie is om die effek van verskeie model parameters op 'n volledige stel spin waarneembares te ondersoek. Die studie toon dat alhoewel die analiseervermoë nie baie sensitief is vir medium effekte nie, die ander spin waarneembares soos byvoorbeeld Dnn waardevolle insig lewer. Daar word voorgestel dat die model verfyn word deur kerndistorsies as ook die meer algemele IA2 model vir die NN interaksie in te sluit.

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22

Keough, James M. "Redox active tyrosines in photosystem II: role in proton coupled electron transfer reactions." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47738.

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Proton coupled electron transfer reactions often involve tyrosine residues, because when oxidized, the phenolic side chain deprotonates. Tyrosine Z (YZ) is responsible for extracting electrons in a stepwise fashion from the oxygen evolving-complex in order to build enough potential to oxidize water. This process requires that each step YZ must deprotonate and reprotonate in order to maintain the high midpoint potential that is necessary to oxidize the oxygen-evolving complex, which makes YZ highly involved in proton coupled electron transfer reactions. In this thesis YZ has been studied within oxygen-evolving photosystem II utilizing electron paramagnetic resonance spectroscopy to monitor the tyrosyl radical that is formed upon light excitation. Kinetic analysis of YZ has shed light on the factors that are important for PSII to carry out water oxidation at the oxygen-evolving complex. Most notably the strong hydrogen-bonding network and the midpoint potential of YZ have been shown to be integral aspects of the water splitting reactions of PSII. By studying YZ within oxygen-evolving PSII, conclusions are readily applied to the native system.

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23

Hodgkiss, Justin M. (Justin Mark) 1978. "Mechanistic studies of photo-induced proton-coupled electron transfer and oxygen atom transfer reactions in model systems." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/38539.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, February 2007.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Vita.
Includes bibliographical references.
Time-resolved optical spectroscopy has been employed for mechanistic studies in model systems designed to undergo photo-induced proton-coupled electron transfer (PCET) and oxygen atom transfer (OAT) reactions, both of which are important to energy conversion chemistry (Chapter I). The effect of coupling proton transfer (PT) to electron transfer (ET) depends on their spatial configuration, thus model PCET systems must control both. Noncovalent amidinium-carboxylate PT interfaces are used assemble an electron D/A pairs (D = donor, A = acceptor), establishing uni-directional ET and PT coordinates. A highly conjugated porphyrin-amidinium derivative bears optical signatures that report on the structure of PT interfaces formed upon association with carboxylate acceptors (Chapter II). PT is supported within the interface and the mediating proton's position is sensitive to the peripheral electronic structure. Transient absorption (TA) spectroscopy is applied to a related porphyrin D---[H+]---A assembly, where ---[H+]--- = amidinecarboxylic acid (Chapter III). Specific probe wavelengths are targeted in order to amplify the optical signatures of PCET over those of competing quenching mechanisms.
(cont.) The observed PCET rates are strongly attenuated compared with comparable covalentlybridged analogues, indicating that the PT interface reduces electronic coupling. Temperature-isotope dependence of the PCET rates reveals an unusual inverse isotope effect at low temperature, which is interpreted in a model of vibrationally-assisted PCET (chapter IV). Hangman porphyrin dyads have been developed to study bi-directional PCET in relation to oxygen activation. ET and PT coordinates are orthogonalized at fixed distances about a FeIII-OH center (Chapters V and VI). TA spectroscopy and electronic structure calculations reveal that the structural reorganization attendant to metal-centered PCET imposes a severe kinetic cost and alternative quenching pathways prevail. Finally, TA spectroscopy has been used to elucidate the mechanism of photocatalytic OAT for bridged diiron [mu]-oxo bisporphyrins (Chapter VII). The [mu]-oxo bond is photo-cleaved to generate a terminal iron(IV) oxo, which undergoes OAT to nucleophilic substrates. OAT rates are maximized when the bridge actively splays the porphyrin subunits apart to present the oxo before reclamping can occur.
by Justin M. Hodgkiss.
Ph.D.

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24

McCoskey, Jacob K. "Sample dehumidification to enhance formaldehyde detection by a proton transfer reaction mass spectrometer." Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Thesis/Summer2009/J_McCoskey_072109.pdf.

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Thesis (M.S. in environmental engineering)--Washington State University, August 2009.
Title from PDF title page (viewed on Aug. 7, 2009). "Department of Civil and Environmental Engineering." Includes bibliographical references (p. 73-76).

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25

Salvitti, Michael Anthony. "N-methyl-6-hydroxyquinolinium : an investigation into the spectroscopy and applications of excited-state proton transfer /." Thesis, Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/24665.

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26

Tian, Feng. "Theoretical Studies on Electrode Reactions in Proton Exchange Membrane Fuel Cells." Case Western Reserve University School of Graduate Studies / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=case1291339549.

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27

Raeker, Tim [Verfasser]. "Full-Dimensional Photodynamics Simulations: From Photoisomerizations to Excited-State Proton Transfer Reactions / Tim Raeker." Kiel : Universitätsbibliothek Kiel, 2018. http://d-nb.info/1161729526/34.

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28

Zhang, Jingxin. "Investigation of CO tolerance in proton exchange membrane fuel cells." Link to electronic thesis, 2004. http://www.wpi.edu/Pubs/ETD/Available/etd-0708104-193007/.

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29

Parada, Giovanny A. "Synthesis of Biomimetic Systems for Proton and Electron Transfer Reactions in the Ground and Excited State." Doctoral thesis, Uppsala universitet, Institutionen för kemi - Ångström, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-251471.

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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.

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30

Liu, Yang, and 刘洋. "Free energy simulations of important biochemical processes." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/196036.

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Free energy simulations have been widely employed to compute the thermodynamic properties of many important biochemical processes. In the first part of this dissertation, two important biochemical processes, protonation/deprotonation of acid in solution and solvation of small organic molecules, are investigated using free energy simulations. Accurate computation of the pKa value of a compound in solution is important and challenging. To efficiently simulate the free energy change associated with the protonation/deprotonation processes in solution, a new method of mixing Hamiltonian, implemented as an approach using a fractional protonin the hybrid quantum mechanics/molecular mechanics (QM/MM) scheme, is developed. This method is a combination of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theoretical and technical details of this method, along with the calculation results of the pKa value of methanol and methanethiol molecules in aqueous solution, are discussed. The simulation results show satisfactory agreement with experimental data. Though the QM/MM method is one of the most useful methods in the modeling of biochemical processes, little attention has been paid to the accuracy of QM/MM methods as an integrated unit. Therefore, the solvation free energies of a set of small organic molecules are simulated as an assessment of ab initio QM/MM methods. It shows that the solvation free energy from QM/MM simulations can vary over a broad range depending on the level of QM theory / basis sets employed. Diffuse functions tend to over-stabilize the solute molecules in aqueous solution. The deviations pose a pressing challenge to the future development of new generation of MM force fields and QM/MM methods if consistency with QM methods becomes a natural requirement. In the second part of the dissertation, the dynamic and energetic properties of two molten globule (MG) protein molecules, α-lactalbumin(α-LA) and monomeric chorismate mutase (mCM) are investigated using molecular dynamics simulations. The exploring of the molecular mechanism of protein folding is a never-settled battle while the properties of MG states and their roles in protein folding become an important question. The MGs show increased side chain flexibility while maintain comparable side-chain coupling compared to the native state, which partially explains the preserving of native-like overall conformation. The enhanced sampling method, temperature-accelerated molecular dynamics (TAMD), is used for the study of the hydrophobic interactions inside both biomolecules. The results suggest that these hydrophobic cores could overcome energy barriers and repack into new conformation states with even lower energies. The repacking of the hydrophobic cores in MGs might be served as a criterion for recognizing the MGs in large class of biomolecules.
published_or_final_version
Chemistry
Doctoral
Doctor of Philosophy

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31

Graige, Michael Scott. "Revealing the mechanisms and energetics of electron and proton transfer reactions in photosynthetic reaction centers from Rb. sphaeroides using molecular probes /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1998. http://wwwlib.umi.com/cr/ucsd/fullcit?p9908502.

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32

Soper, Jake D. "Reactions at nitrogenous ligands on oxidizing group 8 metal centers /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/8589.

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33

Wiley, Jack Scott. "C-H bond activation in iridium complexes /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/8510.

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34

Ortiz, Sánchez Juan Manuel. "Excited state intramolecular proton transfer reactions coupled with non adiabatic processes: electronic structure and quantum dynamical approaches." Doctoral thesis, Universitat Autònoma de Barcelona, 2009. http://hdl.handle.net/10803/3311.

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Els enllaços d'hidrogen són d'importància universal en química i bioquímica. Les propietats dels enllaços d'hidrogen en l'estat electrònic fonamental han estat estudiades durant molt anys. Malgrat tot, molt poc es coneix sobre les reaccions químiques on intervenen enllaços d'hidrogen en els estats electrònics excitats. Una de les reaccions més interessants són les transferències protòniques intramoleculars en estat excitat (ESIPT de les seves sigles en anglès), ja que juguen un paper crucial en una gran varietat de reaccions químiques fotoquímiques de gran rellevància.
Les tècniques més modernes de cinètica química disponibles avui dia, permeten la monitorització dels processos ESIPT fins l'escala de temps del femtosegond. Tot i això, els resultats experimentals acostumen a ser difícils d'interpretar, especialment quan es veuen involucrats processos competitius. Aquests processos addicionals suposen un desafiament extra en l'estudi d'aquestes reaccions. En aquest sentit, la química teòrica i computacional representa una molt versàtil eina de treball, donat l'absolut control que els investigadors poden imposar a sistemes modelitzats aïllats.
Els sistemes moleculars recollits en la present tesi representen exemples directes dels diferents ordres de complexitat que l'estudi teòric (des del punt de vista del càlcul electrònic i dinàmic) del processos ESIPT poden representar: des de la comprensió del aspectes fonamentals del procés, fins a la necessitat d'adoptar estratègies teòriques eficients per tractar la presència de processos no adiabàtics.
Hydrogen Bonds are of universal importance in chemistry and biochemistry. The properties of hydrogen bonds in the electronic ground state have been investigated since long ago. Nevertheless, much less is known about the chemical reactions involving hydrogen bonds in excited electronic states. One of the most interesting reactions are the excited state intramolecular proton transfer (ESIPT) processes, as they play a crucial role in a plethora of photochemical reactions of chemical and biochemical relevance.
The most modern kinetic experimental techniques available today, allow the monitoring of ESIPT processes up to the order of the femtosecond. However, the experimental results are usually difficult to analyze, specially when competitive processes are involved. Those additional processes suppose an extra challenge in the study of this topic. In this sense, theoretical and computational chemistry represents a powerful tool of interpretation, given the absolute control that researchers can impose on modelized isolated systems.
The molecular systems collected in the present thesis represent direct examples of the different orders of complexity that the theoretical study (both from the electronic and dynamical points of view) of ESIPT can represent: from the comprehension of the essentials of the process, to the need of adoption of efficient theoretical strategies to treat the presence of non adiabatic processes.

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Svahn, Emelie. "Molecular machinery of a membrane-bound proton pump : Studies of charge transfer reactions in cytochrome c oxidase." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-108335.

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In cellular respiration, electron transfer from the breakdown of foodstuff is coupled to the formation of an electrochemical proton gradient. This is accomplished through proton translocation by respiratory complexes, and the proton gradient is subsequently used e.g. to drive ATP production. Consequently, proton- and electron-transfer reactions through the hydrophobic interior of membrane proteins are central to cellular respiration. In this thesis, proton- and electron transfer through an aa3-type terminal oxidase, cytochrome c oxidase (CytcO) from Rhodobacter sphaeroides, have been studied with the aim of understanding the molecular proton-transfer machinery of this proton pump. In the catalytic site of CytcO the electrons combine with protons and the terminal electron acceptor O2 to form water in an exergonic reaction that drives proton pumping. Therefore, CytcO must transfer both protons that are pumped and protons for the oxygen chemistry through its interior. This is done through its two proton-transfer pathways, termed the D pathway and the K pathway. Our studies have shown that the protons pumped during oxidation of CytcO are taken through the D pathway, and that this process does not require a functional K pathway. Furthermore, our data suggests that the K pathway is used for charge compensation of electron transfer to the catalytic site, but only in the A2 → P3 state transition. Our data also show that the water molecules identified in the crystal structures of CytcO play an important role in proton transfer through the D pathway. Finally, the effects of liposome reconstitution of CytcO on D-pathway proton transfer were investigated. The results suggest that the membrane modulates the rates of proton transfer through the D pathway, and also influences the extent of electron transfer between redox-active sites CuA and heme a.

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Geibel, Kerstin [Verfasser]. "Search for Proton Emission in Ni-54 and Multi-Nucleon Transfer Reactions in the Actinide Region / Kerstin Geibel." München : Verlag Dr. Hut, 2012. http://d-nb.info/102878466X/34.

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McQueen, Rachel, and n/a. "Axillary odour in apparel textiles." University of Otago. Department of Clothing and Textile Sciences, 2007. http://adt.otago.ac.nz./public/adt-NZDU20070307.120703.

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The axilla is a major source of human body odour from which the characteristic musky, urinous or acidic odours emanate, and are predominantly due to bacterial metabolism of the protein-rich fluid secreted by the apocrine and sebaceous glands located in this area (Senol and Fireman, 1999). Clothing has been implicated in contributing to body odour intensity, possibly even increasing the intensity (Dravnieks, et al., 1968; Shelley, et al., 1953) by the transfer of secretions, skin debris and bacteria from the body to the fabric substrate. Despite much anecdotal evidence indicating that some fibres and fabrics are better at limiting odour intensity than others, there appears to be no published research confirming this. The purpose of this study therefore, was to determine whether fabrics varying in fibre content (cotton, wool, polyester) and fabric knit structure (interlock, single jersey, 1x1 rib) differed in the extent to which they retained and emanated axillary odour following wear, and whether the intensity of odour was linked to the number of bacteria transferred to the fabrics. A procedure for collecting odour on fabrics was developed as was a method for evaluating odour through use of a sensory panel. Total aerobic bacteria and aerobic coryneform bacteria extracted from the fabrics were counted to determine if an association between bacterial counts and fabrics existed. Sensory analysis recognises the unique capability of humans as odour-detecting instruments whereas, instrumental analysis has the potential to offer information on the concentration and identification of axillary compounds, which a human assessor cannot. To investigate a new method for detecting axillary odour on apparel fabrics, proton transfer reaction mass spectrometry (PTR-MS) was used to analyse volatiles emitted from fabrics differing in fibre type. After removal of garments from the human body, axillary odour can be detected on fabrics, with the intensity of odour being strongly influenced by the fibre type from which the fabrics had been made. Polyester fabrics emanated odour of high intensity, cotton that of mid-low odour intensity, and wool fabrics were low odour. Fabric structural properties such as thickness, mass per unit area and openness of knit structure also had an effect on odour intensity. However, as the principal factor influencing odour intensity was fibre, only fabrics characterised by a high intensity (i.e. polyester) were influenced by structural properties. Differences in odour intensity among fabrics were not necessarily related to bacterial numbers, and no �inherent antimicrobial� properties were evident for any of the fabrics. Bacterial populations persisted in all fabrics up to 28 days. A decline in numbers was apparent for high-odour polyester fabrics, while numbers in low-odour wool fabrics remained relatively stable. PTR-MS detected compounds likely to be short-chain carboxylic acids which increased in the headspace above the polyester fabrics after 7 days. However, this increase was not evident for either the wool or cotton fabrics. Therefore, bacterial numbers per se cannot be a predictor of the odour intensity emanating from fabrics at least on the basis of these fabrics and fibres. The intensity of axillary odour emanating from fabrics was found inversely related to fibre hygroscopicity. Keywords:fibre content, fabric structure, axillary odour, sensory analysis, bacteria, corynebacteria, instrumental analysis, PTR-MS

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Wang, Xiaohua. "Characterization of Mesoscopic Fluid-like Films with the Novel Shear-force/Acoustic Microscopy." PDXScholar, 2010. https://pdxscholar.library.pdx.edu/open_access_etds/736.

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The shear force mechanism has been utilized as a distance regulation method in scanning probe microscopes. However, the origin of shear force is still unclear. One of the most important reasons for the shear-force damping is due to the presence of a water contamination layer at the sample surface in ambient conditions. Understanding the behavior of such mesoscopic fluid-like films is of significance for studies of not only scanning probe microscopy but also other complex surface phenomena, such as nanotribology, lubrication, adhesion, wetting, and the microfluidity of biological membranes. This thesis investigates, in particular, the dynamics of mesoscopic fluids confined between two sliding solid boundaries. When fluids are constrained to nanometer-sized regions, their physical properties can greatly differ from those displayed by bulk liquids. To gain an insight into the fundamental characteristics of the confined fluid films, we exploit the versatile capabilities of the novel shear-force/acoustic near-field microscope (SANM), which is able to concurrently and independently monitor the effects of the fluid-mediated interactions acting on both the microscope's probe and the sample to be analyzed. Two signals are monitored simultaneously during each experimental cycle: the tuning fork signal, which is the oscillation amplitude of the probe and gives access to the shear force; and acoustic signal, which is detected by an acoustic sensor placed under the sample. Systematic experiments are carried out to investigate the effects of probe geometry, environmental humidity, and chemical properties of probe and sample surface (water affinity: hydrophobicity or hydrophilicity) on the probe-sample interactions, expressing the influence of the fluid-like contamination films.

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Lepp, Håkan. "Experimental studies of proton translocation reactions in biological systems : Electrogenic events in heme-copper oxidases." Doctoral thesis, Stockholm University, Department of Biochemistry and Biophysics, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-8147.

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Terminal heme-copper oxidases (HCuOs) are transmembrane proteins that catalyze the final step in the respiratory chain - the reduction of O₂ to H₂O, coupled to energy conservation by generation of an electrochemical proton gradient. The most extensively investigated of the HCuOs are the aa₃-type oxidases, to which cytochrome c oxidase (CytcO) belongs, which uses energy released in the O₂-reduction for proton pumping. The bacterial nitric oxide reductases (NORs) have been identified as divergent members of the HCuO-superfamily and are involved in the denitrification pathway where they catalyze the reduction of NO to NO₂. Although as exergonic as O₂-reduction, this reaction is completely non-electrogenic. Among the traditional HCuOs, the cbb₃-type oxidases are the closest relatives to the NORs and as such provide a link between the aa₃ oxidases and the NORs. The cbb₃ oxidases have been shown to pump protons with nearly the same efficiency as the aa₃ oxidases, despite low sequence similarity.

This thesis is focused on measurements of membrane potential generating reactions during catalysis in the CytcO and the cbb₃ oxidase from Rhodobacter sphaeroides, and the NOR from Paracoccus denitrificans, using a time resolved electrometric technique. The pH dependence of the membrane potential generation in CytcO showed that only one proton is taken up and that no protons are pumped, at high pH. An additional kinetic phase was also detected at high pH that presumably originates to from charge-transfer within the K-pathway. Possible reasons for uncoupling, and the extent of charge-transfer, were studied using structural variants of CytcO. The measurements established that electrons and protons are taken up from the same side of the membrane in NOR. In addition, the directionality for proton uptake in cbb₃ oxidase appeared to be dependent on the choice of substrate while proton pumping was indicated to occur only during O₂-reduction.

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Romanini, Simone. "Beyond simple proton transfer processes: domino reactions between 4-substituted indoles and nitroethene as a new gateway to ergot alkaloids." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amslaurea.unibo.it/7325/.

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The multimodal biology activity of ergot alkaloids is known by humankind since middle ages. Synthetically modified ergot alkaloids are used for the treatment of various medical conditions. Despite the great progress in organic syntheses, the total synthesis of ergot alkaloids remains a great challenge due to the complexity of their polycyclic structure with multiple stereogenic centres. This project has developed a new domino reaction between indoles bearing a Michael acceptor at the 4 position and nitroethene, leading to potential ergot alkaloid precursors in highly enantioenriched form. The reaction was optimised and applied to a large variety of substrate with good results. Even if unfortunately all attempts to further modify the obtained polycyclic structure failed, it was found a reaction able to produce the diastereoisomer of the polycyclic product in excellent yields. The compounds synthetized were characterized by NMR and ESIMS analysis confirming the structure and their enantiomeric excess was determined by chiral stationary phase HPLC. The mechanism of the reaction was evaluated by DFT calculations, showing the formation of a key bicoordinated nitronate intermediate, and fully accounting for the results observed with all substrates. The relative and absolute configuration of the adducts were determined by a combination of NMR, ECD and computational methods.

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Mahmoud, Hatem Ahmed. "Resonance Two Photon Ionization Study of Binary Clusters of Styrene with Polar Molecules." VCU Scholars Compass, 2003. http://scholarscompass.vcu.edu/etd/983.

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One-color resonance two-photo ionization (R2PI) spectra of mixed clusters of styrene molecule (S) with polar molecules [water (W), methanol (M), ethanol (E), and trifuoroethanol (T)] were measured through the S1←S0 transition of the styrene molecule. The spectra reveal a rapid increase in complexity with the number of polar molecules in the cluster, associated with van der Waal modes and isomeric forms. The spectral shifts of the cluster origins from the S1-S0 transition of the bare styrene molecule reflect the nature of the intermolecular interactions within the binary clusters. The obtained R2PI spectra xv were compared with the spectra of the analogous benzene containing clusters. The styrene-water and the styrene-methanol complexes exhibited very different spectral shifts and structures as compared to the benzene-water and benzene-methanol complexes, respectively. The favorable interactions of polar molecules with the olefin group of styrene may explain the strong inhibition effects of exerted by small concentrations of water and alcohols on the cationic polymerization of styrene. Size-specified intracluster proton transfer reactions were observed for mixed clusters of styrene dimer with water, methanol and ethanol molecules. It was proposed that the polar molecules tend to aggregate around the olefin center, which promotes the transfer of the charge from the propagating chain to the hydrogen-bonded polar molecules subcluster. The minimum number of polar molecules required for a proton transfer to take place exothermically depends on the proton affinity of the polar molecules subcluster. The estimated upper limit value for the proton affinity of styrene dimer radical was evaluated based on the energetic of the proton transfer reaction to be ≤ 220.4 kcal/mol. No intracluster reaction was observed for styrene-trifluoroethanol (STn) system. In order to provide a comparison between the styrene and benzene systems, the benzene-ethanol (BEn) and benzene-trifluoroethanol (BTn) clusters were studied by using the R2PI technique via the 6¹0 transition of the benzene molecule. Both dissociative electron transfer and dissociative proton transfer reactions were observed within the BEn clusters, where n = 2 and 3, respectively. Proton transfer reactions were observed following dissociative electron transfer reactions within the (BTn) clusters, where n = 4, to generate the protonated clusters (H+Tn).

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Offenbacher, Adam R. "Protein structural changes and tyrosyl radical-mediated electron transfer reactions in ribonucleotide reductase and model compounds." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/39473.

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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.

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Li, Zhao. "The Kinetics and Mechanisms of Some Fundamental Organic Reactions of Nitro Compounds." DigitalCommons@USU, 2012. https://digitalcommons.usu.edu/etd/1407.

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The central topic of this dissertation is to seek the answer to the question: Is the single transition state model appropriate for (1) the proton transfer reactions of nitroalkanes and (2) the aromatic nucleophilic reactions of trinitroarenes? If not, what are the real mechanisms? This objective has been accomplished by careful kinetic and mechanistic studies which take advantage of modern digital acquisition of absorbance - time data, combined with extensive new data analysis of results from pseudo-first-order kinetic measurements. Several new analysis procedures for pseudo-first-order kinetics that are capable of distinguishing between single-step and multi-step mechanisms have been introduced and intensively confirmed during the application in the kinetic study of the target reactions. The procedures include (1) half-life dependence of apparent rate constant, (2) sequential linear pseudo-first-order correlation, (3) approximate instantaneous rate constant analysis, and (4) time-dependent apparent kinetic isotope effects. Various conventional and nonconventional pseudo-first-order kinetic analyses of the reactions of nitroalkanes in aqueous solutions revealed that the reactions are complex and involve kinetically significant intermediates. The spectral evidence for the formation of reactive intermediates was obtained by carrying out the kinetic experiments at the isosbestic points where changes in reactant and product absorbance cancel. The apparent deuterium kinetic isotope effects studies indicated that the deuterium kinetic isotope effects are not associated with the formation of the intermediates. The observations of anomalous Brønsted exponents previously found for this reaction series could be rationalized well with the complex mechanisms proposed in this work, which indicate that the nitroalkane anomaly does not exist, but arises from an interpretation based upon the incorrect assumption that the reactions follow a simple one-step mechanism. Simulations revealed that the generally accepted competitive mechanism was not appropriate to describe the Meisenheimer complex formation during the reaction of 2,4,6-trinitroanisole with methoxide ion in methanol. This conclusion is supported by the conventional pseudo-first-order kinetic analysis. A reversible consecutive mechanism that accounts for the kinetic behavior has been proposed, which involves an intermediate dianion complex that is formed reversibly from the initial 1,3-σ-complex, and then eliminates methoxide ion to form the 1,1-σ-complex product.

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Dilbeck, Preston Lee. "Proton transfer reactions in photosynthetic water oxidation| Second sphere ligands of the manganese cluster modulate the water oxidation mechanism of photosystem ii." Thesis, Oklahoma State University, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3614379.

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In the D1-D61N mutant, it was possible to resolve a clear lag phase prior to the appearance of O2, indicating formation of an intermediate before onset of O2 formation. The lag phase and the photochemical miss factor were more sensitive to isotope substitution in the mutant indicating that proton efflux in the mutant proceeds via an alternative pathway. The results are discussed in comparison with earlier results obtained from the substitution of CP43-Arg357 with lysine and in regards to hypotheses concerning the nature of the final steps in photosynthetic water oxidation. These considerations lead to the conclusion that proton expulsion during the initial phase of the S3-S0 transition starts with the deprotonation of primary catalytic base, probably CP43-Arg357, followed by efficient proton egress involving the carboxyl group of D1-D61 in a process that constitutes the lag phase immediately prior to O2 formation chemistry. The asparagine, phenylalanine and threonine substitutions to D1-V185 were able to accumulate significant levels of charge separating PSII. Of the three substitutions the phenylalanine substitution was the most severe with a complete inability to evolve oxygen, despite being able to accumulate Photosystem II and to undergo stable charge separations. The threonine substitution had no apparent effect on oxygen evolution other than a 40% reduction in the steady state rate of O2 production compared to type Synechocystis, which can be attributed to that mutants reduced ability to accumulate PSII. The asparagine substitution produced the most complex phenotype. While still able to evolve oxygen, it does so less efficiently than wild type PSII, with a miss factor 4% higher than wild type Synechocystis. The substitution on D1-Val185 with asparagine also decreased the t1/2 of O2 release from thylakoid membranes from 1.2 ms to 10.0 ms and decreased the t1/2 lag phase prior to the onset of O2 release to 2.8 ms. The combination of a long lag period and a decreased rate of O2 release can also be observed in the D1-D61N mutant strains of Synechocystis and in PSII centers in which chloride has been replaced by iodide.

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Medina, Ramos Jonnathan. "ACID-BASE CATALYSIS IN PROTON-COUPLED ELECTRON TRANSFER REACTIONS (PCET): THE EFFECTS OF BRÖNSTED BASES ON THE OXIDATION OF GLUTATHIONE AND HYDROQUINONE." VCU Scholars Compass, 2012. http://scholarscompass.vcu.edu/etd/2918.

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This thesis presents the results and discussion of the investigation of the effects of Brönsted bases on the kinetics and thermodynamics of two proton-coupled electron transfer processes: the mediated oxidation of glutathione and the electrochemical oxidation of hydroquinone. Proton-coupled electron transfer (PCET) is the name given to reactions that involve the transfer of electron(s) accompanied by the exchange of proton(s). PCETs are found in many chemical and biological processes, some of current technological relevance such as the oxygen reduction reaction in fuel cells, which involves the transfer of four electrons and four protons (4e-, 4H+); or the splitting of water into protons (4H+), electrons (4e-) and oxygen (O2) efficiently achieved in photosynthesis. The study of PCET mechanisms is imperative to understanding biological processes as well as to developing more efficient technological applications. However, there are still many unanswered questions regarding the kinetic and thermodynamic performance of PCETs, and especially about the effect of different proton acceptors on the rate and mechanism of PCET reactions. This study aimed to investigate the effect of Brönsted bases as proton acceptors on the kinetics and thermodynamics of two model PCET processes, the oxidation of glutathione and hydroquinone. The analysis presented in this thesis provides insight into the influence of different proton acceptors on the mechanism of PCET and it does so by studying these reactions from a different angle, that one of the acid-base catalysis theory which has been successfully applied to the investigation of numerous chemical reactions coupled to proton transfer. We hope future research of PCETs can benefit from the knowledge of acid-base catalysis to better understand these reactions at a molecular level.

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46

Polshakov, Dmitrii Arkadyevich. "Ultrafast spectroscopy and dynamics of nitrenes and carbenes." Columbus, Ohio : Ohio State University, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1130968887.

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Rini, Matteo. "Femtosecond mid-infrared spectroscopy of elementary photoinduced reactions." Doctoral thesis, [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=970187912.

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Walmsley, Ryan Steven. "An investigation into the antidiabetic and catalytic properties of oxovanadium(IV) complexes." Thesis, Rhodes University, 2012. http://hdl.handle.net/10962/d1004978.

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In part 1 of this thesis, the antidiabetic activity of a series of novel oxovanadium(IV) complexes was investigated. A range of bidentate N,O-donor ligands, which partially mimic naturally occurring bioligands, were prepared and reacted with the vanadyl ion to form the corresponding bis-coordinated complexes. Initially, 2-(2ˊ-hydroxyphenyl)-1R-imidazoline (where R = H, ethyl and ethanol) ligands were prepared. The aqueous pH-metric chemical speciation was investigated using glass electrode potentiometry which allowed for the determination of protonation and stability constants of the ligands and complexes, respectively. The species distribution diagrams generated from this information gave an indication of how the complexes might behave across the broad pH range experienced in the digestive and circulatory systems. This information was used to create an improved 2nd generation of ligands that were constructed by combining the imidazole and carboxylic acid functionalities. These corresponding bis[(imidazolyl)carboxylato]-oxovanadium(IV) complexes displayed a broader pH-metric stability. Both sets of complexes improved glucose uptake and reduced coagulation in vitro. In part 2 of this thesis, a range of homogeneous and heterogeneous oxovanadium(IV) catalysts were prepared. Firstly, Merrifield beads were functionalized with ligands from Part 1 and then reacted with vanadyl sulfate to afford the corresponding heterogeneous catalysts. These displayed promising catalytic activity for the peroxide facilitated oxidation of thioanisole, styrene and ethylbenzene as well as the oxidative bromination of phenol red. Smaller imidazole-containing beads with higher surface areas than the Merrifield beads were prepared by suspension polymerization. These beads similarly demonstrated excellent catalytic activity for the oxidation of thioanisole and were highly recyclable. In attempt to increase the exposed catalytic surface area, while retaining the ease of separation achieved in the before mentioned systems, micron to nano sized electrospun fibers containing coordinating ligands were fabricated. The corresponding oxovanadium(IV) functionalized fibers were applied to the oxidation of thioanisole using a continuous flow system. The flexible and porous nature of the fiber mats was well suited to this approach. After optimization of the reactant flow rate and catalyst amount, near quantitative (> 99%) oxidation was achieved for an extended period. In addition, leaching of vanadium was mitigated by modification of the attached ligand or polymer material.

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Bruylants, Gilles. "Etude par calorimétrie à titrage isotherme (ITC) et spectroscopie de résonnance magnétique nucléaire (RMN) des effets de protonation liés à l'interaction entre l'alpha-chymotrypsine et la proflavine / Gilles Bruylants." Doctoral thesis, Universite Libre de Bruxelles, 2005. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210977.

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Le nombre de cibles potentielles pour la conception de nouvelles molécules à activité thérapeutique ne cesse de croître. Pour chaque cible, il est nécessaire d’identifier des molécules actives et de les optimiser afin d’atteindre l’affinité et la sélectivité recherchées. Ces nouveaux défis accentuent la nécessité d’améliorer notre compréhension des facteurs qui mènent à la reconnaissance moléculaire entre une drogue potentielle et une macromolécule biologique, et particulièrement des facteurs énergétiques à la base de la stabilisation d’un complexe d’interaction. Dans le cadre de ce travail, nous nous sommes intéressés à l’effet que pouvaient avoir les équilibres de protonation/déprotonation des résidus ionisables d’une protéine sur les paramètres thermodynamiques caractérisant la complexation d’un ligand. Dasns ce but, nous avons étudié l’interaction entre l’α-chymotrypsine et un de ses inhibiteurs compétitifs, la proflavine. Cette protéine est représentative d’un nombre important d’enzymes présentant le même mécanisme catalytique. La compréhension des facteurs qui régissent les équilibres de protonation/déprotonation des résidus ionisables présents dans son site actif ainsi que de l’effet sur ceux-ci de l’interaction avec des ligands est d’une importance primordiale pour le développement d’inhibiteurs plus sélectifs de ces protéases.

Cette étude s’est essentiellement composée de trois volets. (i) La réalisation d’un modèle du complexe d’interaction afin de confronter des données structurales aux données expérimentales recueillies. (ii) L’étude de l’interaction entre l’α-chymotrypsine et la proflavine par spectroscopie de Résonance Magnétique Nucléaire (RMN) afin de mettre en évidence les résidus ionisables dont les équilibres de protonation/déprotonation sont influencés par la complexation du ligand. (iii) L’étude de la thermodynamique de l’interaction par Calorimétrie à Titrage Isotherme (ITC) et spectroscopie d’absorption en fonction de l’état d’ionisation des résidus identifiés par l’étude RMN.

Le modèle du complexe d’interaction entre l’α-chymotrypsine et la proflavine a été réalisé sur base de la structure cristallographique du complexe entre cet inhibiteur et une protéase apparentée à la chymotrypsine, la thrombine. Il ressort de l’analyse du modèle obtenu que la proflavine est profondément enfouie dans le subsite S1 de l’enzyme et présente une très grande complémentarité de surface avec cette poche hydrophobe. Nous avons également pu constater la présence de plusieurs molécules d’eau immobilisées au sein du complexe, et d’une molécule en particulier faisant office de relais de liens-H.

L’étude de l’interaction entre l’α-chymotrypsine et la proflavine par RMN du 1H a été précédée par une étude de l’effet du degré de maturité de l’enzyme sur les interactions liant les différents résidus composant la triade catalytique (Asp102, His57 et Ser195). Lors de l’activation du précurseur inactif de l’enzyme, le chymotrypsinogène, vers la forme mature, l’α-chymotrypsine, il semble en effet que le lien-H entre le NH&949;2 de l’His57 et le Oγ de la Ser195 soit affaibli, contrairement à celui qui relie le NHδ1 de cette même histidine au Oδ1 de l’Asp102. Nous rapportons pour la première fois l’observation de l’influence de la protonation de l’Asp102 sur les déplacements chimiques des protons NHδ1 et NH&949;2 de l’His57. L’étude de l’interaction entre l’α-chymotrypsine et la proflavine par RMN, nous a permis de mettre en évidence l’effet de la complexation du ligand sur l’état d’ionisation des résidus His57 et Asp102 de la triade catalytique, les pKa de ces résidus dans l’enzyme libre valant respectivement 7 et approximativement 4.

Les paramètres thermodynamiques de l’interaction α-chymotrypsine - proflavine et des différents équilibres de protonation/déprotonation qui y sont liés ont été obtenus par spectroscopie d’absorption et ITC. Cette dernière technique constitue un outil précieux pour l’étude d’interactions moléculaires car il s’agit de la seule technique expérimentale permettant la mesure directe de l’enthalpie d’interaction. Lorsque des équilibres de protonation/déprotonation sont thermodynamiquement liés à l’interaction, il s’agit également de la seule technique permettant la quantification de ces effets. En mesurant la constante d’affinité et l’enthalpie d’interaction observées à différents pH et dans différents tampons, nous avons pu, sur base du modèle obtenu par RMN, déterminer les paramètres thermodynamiques intrinsèques des différents équilibres.

La corrélation entre les données thermodynamiques obtenues par ITC et spectroscopie d’absorption et les données structurales obtenues par RMN et sur base de l’analyse du modèle du complexe d’interaction, nous a permis de rationaliser les facteurs à la base de l’interaction préférentielle de l’inhibiteur avec une des formes de l’enzyme. L’interaction entre l’α-chymotrypsine et la proflavine est la plus favorable lorsqu’à la fois l’His57 et l’Asp102 sont déprotonnés. Cette interaction est caractérisée par un terme enthalpique favorable et un terme entropique légèrement défavorable. Ce dernier terme s’expliquerait en partie par l’immobilisation dans le site d’interaction de plusieurs molécules d’eau. L’affinité entre l’α-chymotrypsine et la proflavine diminue lorsque l’His57 se protonne. La répulsion électrostatique entre les charges positives de la proflavine et de l’His57 est vraisemblablement un des facteurs permettant d’expliquer cette diminution de la constante d’affinité. Nous n’avons pu mettre en évidence d’interaction entre ces deux molécules dès lors que l’Asp102 est protonné, malgré que ce résidu soit situé relativement loin de la proflavine dans le complexe. Il s’agit donc d’un effet indirect, probablement relayé par l’His57. Tant que l’Asp102 est déprotonné, sa charge négative compenserait la charge positive de l’His57 et réduirait la répulsion électrostatique avec la proflavine, ce qui n’est plus le cas lorsque l’aspartate se protonne.
Doctorat en sciences appliquées
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50

Le, Crom Benjamin. "Étude de l'appariement neutron-proton dans les noyaux instables N=Z par réactions de transfert." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS007/document.

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Abstract:

Le noyau est généralement décrit comme un ensemble de protons et de neutrons liés dans un potentiel de champ moyen. Cependant afin d'obtenir une meilleure description, il convient de tenir compte des interactions locales dont principalement l'appariement. Les appariements neutron-neutron et proton-proton sont assez bien étudiés alors que ce n'est pas le cas de l'appariement neutron-proton. Celui-ci peut être soit isovectoriel similaire à l'appariement nn/pp, soit isoscalaire et donc dans ce cas vraiment méconnu. La surliaison des noyaux N=Z pourrait être une manifestation de l'appariement np.Nous avons effectué l'étude de l'appariement np par réactions de transfert de paires np. Dans ce cas il est attendu que la section efficace de transfert de paires np soit augmentée en présence d'un appariement np important. L'appariement np devrait être important dans les noyaux N=Z avec des orbitales de J élevé. Or, des faisceaux de ces noyaux ne sont accessibles que depuis le développement des installations de faisceaux radioactifs.Nous avons effectué notre expérience au GANIL (Caen) avec un montage permettant une détection des produits issus de la réaction de transfert (p, ³ He). Cette réaction met en jeu à la fois des paires np isovectorielles et isoscalaires. Nous avons utilisé des faisceaux de ⁵⁶ Ni et de ⁵²Fe permettant d'observer l'évolution de l'appariement np avec l'occupation de la couche 0f7/2.Tout d'abord, nous avons analysé les données issues de la réaction ⁵⁶Ni(p,d)⁵⁵Ni et extrait des résultats que nous avons comparé à ceux existants. Cette démarche a permis de valider la procédure d'analyse des données.Après analyse des données issues de la réaction ⁵⁶Ni(p,3He)⁵⁴Co, nous avons extrait les populations des états du ⁵⁴Co qui donnent des informations sur l'intensité relative des deux types d'appariement np pour le noyau ⁵⁶Ni et montrent que l'appariement np isovectoriel est dominant dans ce noyau.De plus, dans le cadre d'un développement d'un futur détecteur de particules chargées, un travail de R&D sur la discrimination des particules légères par la forme des signaux a été réalisé et est présenté
A nucleus is described as a set of independent neutrons and protons linked by a mean-field potential. However, in order to have a better description one needs to take in account some residual interactions such as pairing. Neutron-neutron and proton-proton pairings are well-studied but neutron-proton pairing is not well-known. np pairing can be isovector pairing such as nn and pp pairing or isoscalar which is yet unknown. Overbinding of N=Z nuclei could be a manifestation of np pairing.We have studied np pairing through transfer reactions. In this case, the cross-section of np pair transfer is expected to be enhanced in the presence of important np pairing. np pairing is expected to be important in N=Z nuclei with high J orbitals. Since the development of radioactive beam facilities, such beams are only available.The experiment was performed at GANIL with an efficient set-up so as to detect products from the (p,³He) transfer reaction. This reaction is affected by isovector and isoscalar np pairing. We used ⁵⁶Ni and ⁵²Fe beams so as to see the effect of the occupancy of 0f7/2 shell on the np pairing.First, we analysed the data from the ⁵⁶Ni(p,d)⁵⁵Ni reaction and we compared the results with the literature to validate analysis procedure.After analysing data from the ⁵⁶Ni(p,3He)⁵⁴Co reaction and extracting the population of the various states of ⁵⁴Co, we obtained information about the relative intensity between isoscalar and isovector np pairing in ⁵⁶Ni showing the predominance of isovector np pairing in this nucleus .Moreover, in the framework of developing a new charged particle detector, R&D on the discrimination of light nuclei using pulse shape analysis was performed and is presented

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