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.

<p>The thesis contains two directions in the simulations of biomolecular systems. The first part (Chapter 2 - Chapter 4) mainly focuses on the simulations of electron transfer processes in condensed phase; the second part (Chapter 5 - Chapter 6) investigates the conformational sampling of polysaccharides and proteins. Electron transfer (ET) reaction is one of the most fundamental processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, calculating the accurate kinetic and dynamic properties of ET reactions is challenging but extremely useful. Based on the Marcus theory for thermal ET in weak coupling limit, we combined the rigorous ab initio quantum mechanical (QM) method and well-established molecular mechanical (MM) force field and developed an approach to directly calculate a key factor that affects the ET kinetics: the redox free energy. A novel reaction order parameter fractional number of electrons (FNE) was used to characterize the ET progress and to drive the QM/MMMD sampling of the nonadiabatic free energy surface. This method was used for two aqueous metal cations, iron and ruthenium in solution, and generated satisfactory results compared to experiments. In order to further reduce the computational cost, a QM/MM-minimum free energy path (MFEP) method is implemented and combined with the FNE in the calculation of redox free energies. The calculation results using QM/MM-MFEP+FNE generated identical results as the direct QM/MM-MD method for the two metal cations, demonstrating the consistency of the two different sampling strategy. Furthermore, this new method was applied to the calculation of organic molecules and enhanced the computational efficiency 15-30 times than the direct QM/MM-MD method, while maintaining high accuracy. Finally, I successfully extended the QM/MM-MFEP+FNE method to a series of redox proteins, azurin and its mutants, and obtained very accurate redox free energy differences with relative error less than 0.1 eV. The new method demonstrated its excellent transferability, reliability and accuracy among various conditions from aqueous solutions to complex protein systems. Therefore, it shows great promises for applications of the studies on redox reactions in biochemistry. In the studies of force-induced conformational transitions of biomolecules, the large time-scale difference from experiments presents the challenge of obtaining convergent sampling for molecular dynamics simulations. To circumvent this fundamental problem, an approach combining the replica-exchange method and umbrella sampling (REM-US) is developed to simulate mechanical stretching of biomolecules under equilibrium conditions. Equilibrium properties of conformational transitions can be obtained directly from simulations without further assumptions. To test the performance, we carried out REM-US simulations of atomic force microscope (AFM) stretching and relaxing measurements on the polysaccharide pustulan, a (1&rarr;6)-&beta;-D-glucan, which undergoes well-characterized rotameric transitions in the backbone bonds. With significantly enhanced sampling convergence and efficiency, the REMUS approach closely reproduced the equilibrium force-extension curves measured in AFM experiments. Consistent with the reversibility in the AFM measurements, the new approach generated identical force-extension curves in both stretching and relaxing simulations, an outcome not reported in previous studies, proving that equilibrium conditions were achieved in the simulations. In addition, simulations of nine different polysaccharides were performed and the conformational transitions were reexamined using the REM-US approach. The new approach demonstrated consistent and reliable performance among various systems. With fully converged samplings and minimized statistical errors, both the agreement and the deviations between the simulation results and the AFM data were clearly presented. REM-US may provide a robust approach to modeling of mechanical stretching on polysaccharides and even nucleic acids. However, the performance of the REM-US in protein systems, especially with explicit solvent model, is limited by the large system size and the complex interactions. Therefore, a Go-like model is employed to simulate the protein folding/unfolding processes controlled by AFM. The simulations exquisitely reproduced the experimental unfolding and refolding force extension relationships and led to the full reconstruction of the vectorial folding pathway of a large polypeptide, the 253-residue consensus ankyrin repeat protein, NI6C. The trajectories obtained in the simulation captured the critical conformational transitions and the rate-limiting nucleation event. Together with the AFM experiments, the coarse-grained simulations revealed the protein folding and unfolding pathways under the mechanical tension.</p> / Dissertation

In recent years, the conventional Flash memory with floating structure is expected to reach physical limits as devices scaling down in near future. In order to overcome this problem, alternative memory technologies have been widely investigated. And the resistance random access memory (RRAM) has attracted extensive attention for the application in next generation nonvolatile memory, due to the excellent memory property including lower consumption of energy, lower operating voltage, higher density, fast operating speed, simple structure, higher endurance, retention and process compatibility with CMOS. In this study, the tungsten-based oxide is chosen as RRAM switching layer because the tungsten is compatible with the present complementary metal oxide semiconductor (CMOS) process. The Pt/WOX/TiN structure device cells had the resistance switching property successfully. However, the experiment result revealed the inferior resistance switching property. The resistance switching characteristic of the WOX thin film is extremely unstable, it is impossible to become the products. Compared with WOX, the resistance switching property of WSiOX RRAM device is improved substantially such as stability of resistance states and reliability of device. In second parts, we purposed two methods to enhance the device switching characteristic, including controlling the filament formation/ interruption in the W doped SiOX layer and restricting oxygen movement in the WSiON layer. Finally, the transport mechanisms of carrier is analyzed and researched from the current-voltage (I-V) switching characteristic of the device. A designed circuit was used in this study to accurately observe the resistance switching process with a pulse generator and oscilloscope, which reveals that the switching process is related to both time and voltage. The oxygen movement will drift in the low temperature due to the electrical field and restricted the crystal lattice vibration. But, it will diffuse through thermal dynamics in the high temperature.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20630号 / 工博第4368号 / 新制||工||1679(附属図書館) / 京都大学大学院工学研究科物質エネルギー化学専攻 / (主査)教授 安部 武志, 教授 阿部 竜, 教授 作花 哲夫 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

According to previous research, students show difficulties in learning redox reactions. By the historical development different redox models exist to explain redox reactions, the oxygen model, the hydrogen model, the electron model and the oxidation number model. This thesis reports about three studies concerning conceptions held by secondary school students of redox reactions. A textbook analysis is also included in the thesis. The first study was an investigation of the students’ use of redox models in inorganic contexts, their use of the activity series of metals, and the students’ ability to transfer redox knowledge. Then the students’ work with an open-ended biochemical task, where the students had access of the textbook was studied. The students talk about redox reactions, the questions raised by the students, what resources used to answer the questions and what kind of talk developed were investigated. A textbook analysis based on chemistry books from Sweden and one book from England was performed. The redox models used as well as the dealing with redox related learning difficulties was studied. Finally, the students’ conceptions about redox in inorganic, organic and biochemistry after completed chemistry courses were studied. The results show that the students were able to use the electron model as a tool to explain inorganic redox reactions and the mutuality of oxidation and reduction was fundamental. The activity series of metals became a tool for the prediction of reducing agent in some reactions. Most of the students rejected that oxygen is a prerequisite for a redox reaction. In the biochemical task the resource most used to answer the raised questions were the students’ consultation of the textbook – together or individually. Most questions resulted in short answers and the majority of these questions were answered. Questions concerning redox were analysed by the students and integrated into a chemical context but they could neither identify the substances oxidised or reduced nor couple the concepts to transfer of hydrogen atoms. The majority of these redox questions became unanswered. The textbook helped the students to structure a poster as well as to answer basic chemistry questions. For questions about organic and biochemical redox, the book was of no help. The textbook analysis showed that all historical redox models are used. Different models are used in inorganic, organic and biochemistry. The mutuality of oxidation and reduction is treated differently in subject areas. The textbooks did not help the reader linking the different redox models that were used. Few redox-related learning difficulties are addressed in the books. After completed chemistry courses the students had major problems to justify a redox reaction explained by transfer of hydrogen atoms both in the organic and biochemistry examples.

In der vorliegenden Arbeit wurde die Methode der magnetischen Kernspinresonanz (NMR) eingesetzt, um beim Schadstoffabbau stattfindende Prozesse und geochemische Reaktionen zerstörungs- und beprobungsfrei zu untersuchen. Dies ist möglich, da die gelösten Elektronenakzeptoren Sauerstoff und Eisen paramagnetisch sind und somit einen Ein uss auf die NMRRelaxationszeiten ausüben. Der lineare Zusammenhang zwischen der gelösten Sauerstoff- beziehungsweise Eisen-Konzentration und den NMR-Relaxationsraten 1/T1 und 1/T2 wurde quantifiziert. Weiterhin wurde der bereits bekannte Einfluss der Matrixoberflächen von porösen Medien auf die Relaxation von Wasser nachgewiesen. Die paramagnetischen Zentren auf Sandoberflächen führen ebenfalls zu einer Verkürzung der Relaxationszeiten. Es wurde gezeigt, dass die kleinsten Korngrößen der verwendeten Sande den größten Einfluss auf die Oberflächenrelaxation haben. Wird die Oberflächenrelaxation berücksichtigt, ist auch in porösen Medien die ermittelte lineare Abhängigkeit der Relaxationszeiten von der Ionenkonzentration anwendbar, um den Gehalt an gelösten paramagnetischen Ionen aus Relaxationsmessungen zu ermitteln. Beispielhaft wurde der Anstieg der Eisen(III)-Konzentration in der Porenlösung von natürlichen Sanden infolge der Auflösung eisenhaltiger Mineralien von den Oberflächen zeitlich und räumlich detailliert betrachtet. Eine durchgeführte Modellierung zeigte, dass das Reaktionssystem zu Beginn der Reaktion von der Diffusion dominiert wird, am Ende dann die Reaktionsgeschwindigkeit der bestimmende Parameter ist. Die beim biologischen Schadstoffabbau auftretenden Redoxprozesse des Eisens wurden durch rein chemische Reaktionen unter Verwendung von Oxidations- und Reduktionsmitteln simuliert. Die zeitlich und räumlich detaillierte Beobachtung des Anstiegs beziehungsweise des Abfalls der gelösten Eisen(III)-Konzentration in der (Poren-)Lösung war mit NMR-Relaxometrie trotz der Schnelligkeit der Reaktionen möglich. Mit Hilfe der anschliessenden Modellierung wurde der wichtige Einfluss des pH-Wertes auf den genauen Ablauf der Reaktionen deutlich gemacht. Nur in sehr sauren pH-Bereichen (pH < 3) liegen die Eisen(III)-Ionen in Lösung vor. Weiterhin wurde der Einfluss der Mikroorganismen selbst auf die NMR-Relaxations- und Diffusionsmessungen untersucht. Im Rahmen dieser Arbeit wurde an Medien mit Lactobacillus und Penicillium eine Verschiebungen in den Relaxationszeitverteilungen hin zu kleineren Relaxationszeiten gemessen. Dies basiert auf der bereits bekannten Verringerung der Mobilität der Spins innerhalb der Biomasse. Für Bakterien von Geobacter metallireducens konnte erstmals der Verbrauch von Eisen(III)-Ionen durch Reduktion während des Wachstum anhand der ansteigenden T2-Relaxationszeit gezeigt werden.

A multi-functional RuO₂ nanoparticle-embedded mesoporous carbon-coated separator is used as an electrocatalytic and adsorbing polysulphide-net to enhance the redox reaction of migrating polysulphides, to improve active material utilization and boost the electrochemical performance of lithium–sulphur batteries.

The kinetic and mechanistic features of a new series ofplatinum-thallium cyano compounds containing a direct andunsupported by ligands metal-metal bond have been studied insolution, using standard mix–and–measurespectrophotometric technique and stopped–flow method.These reactions are interpreted as oxidative addition of the cspecies to the square planar Pt(CN)42-complex. Each of these processes was found to befirst-order in Pt(CN)42-, the corresponding TIIIIcomplex and a cyanide ion donating species whichacts as a catalyst. Both di- and trinuclear complexes werestudied, and the kinetically significant thallium complexes intheir formation and the catalytically active cyanide sourcesare as follows: [(CN)5PtTl(CN)3]3-: Tl(CN)4–(alkaline region), Tl(CN)3(slightly acidic region) and CN–; [(CN)5Pt–Tl(CN)]–: Tl(CN)2+and Tl(CN)2+; [(CN)5Pt–Tl–Pt(CN)5]3-: [(CN)5Pt–Tl(CN)]–and HCN. Appropriatemechanisms were postulated for the overall reactions in allcases, which include i) metal–metal bond formation stepand ii) coordination of an axial cyanide ion to the platinumcenter. Two experimentally indistinguishable kinetic modelswere proposed for the formation of the dinuclear complexeswhich are different in the sequence of the two steps. In thecase of the trinuclear complex, experimental evidence isavailable to exclude one of the alternative reaction paths, andit was proven that the metal–metal bond formation precedesthe axial cyanide coordination. The cyanide ligands coordinated to TIIIIin the Pt–Tl complexes could be replacedsuccessfully with aminopolycarboxylates e.g.: mimda2-, nta3-, edta4-. The [(CN)5Pt–Tl(edta)]4-complex, with a direct metal–metal bond hasbeen prepared in solution by two different reactions: a)dissolution of [(CN)5Pt–Tl](s) in an aqueous solution of edta, b)directly from Pt(CN)42-and Tl(edta)(CN)2-. The decomposition reaction is greatlyaccelerated by cyanide and significantly inhibited by edta. Itproceeds through the [(CN)5Pt–Tl(CN)3]3-intermediate. The formation of [(CN)5Pt–Tl(edta)]4-can proceed via two different pathways dependingon the ratio of the cyanide to the edta ligand concentrations.The’direct path’at excess of edta means theformation of intermediate[(CN)4Pt···Tl(CN)(edta)]4-, followed by a release of the cyanide from theTl–centre followed by coordination of a cyanide from thebulk to the Pt–centre of the intermediate. The’indirect path’dominates in the absence of extraedta and the formation of the Pt–Tl bond occours betweenPt(CN)42-and Tl(CN)4–. Homoligand MTl(CN)4(M = TlI, K, Na) and, for the first time, Tl(CN)3species have been synthesized in the solid stateand their structures solved by single crystal X–raydiffraction method. Interesting redox processes have been foundbetween TIIIIand CN–in non–aqueous solution and in Tl2O3-CN–aqueous suspension. In the crystal structureof Tl(CN)3·H2O, the thallium(III) ion has a trigonal bypiramidalcoordination geometry with three cyanides in the trigonalplane, while an oxygen atom of the water molecule and anitrogen atom from a cyanide ligand attached to a neighboringthallium complex, form a linear O–Tl–N fragment.Cyanide ligand bridges thallium units forming an infinitezigzag chain structure. Among the thallium(III) tetracyanocompounds, the isostructural M[Tl(CN)4](M = Tl and K) and Na[Tl(CN)4]·3H2O crystallize in different crystal systems, but thethallium(III) ion has in all cases the same tetrahedralgeometry in the [Tl(CN)4]–unit. Three adducts of mercury(II) (isoelectronic with TIIII) (K2PtHg(CN)6·2H2O, Na2PdHg(CN)6·2H2O and K2NiHg(CN)6·2H2O) have been prepared from Hg(CN)2and square planar transition metal cyanides MII(CN)42-and their structure have been studied by singlecrystal X–ray diffraction, XPS and Raman spectroscopy inthe solid state. The structure of (K2PtHg(CN)6·2H2O consists of strictly linear one dimensional wireswith PtIIand HgIIcenters located alternately, dHg–Pt= 3.460 Å. The structure of Na2PdHg(CN)6·2H2O and K2NiHg(CN)6·2H2O can be considered as double salts, the lack ofhetero–metallophilic interaction between both the HgIIand PdIIatoms, dHg–Pd= 4.92 Å, and HgIIand NiIIatoms, dNi–Pd= 4.60 Å, seems obvious. Electronbinding energy values of the metallic centers measured by XPSshow that there is no electron transfer between the metal ionsin all three adducts. In solution, experimental findingsclearly indicate the lack of metal–metal bond formation inall studied HgII–CN-–MII(CN)42-systems (M = Pt, Pd and Ni). It is in contrary tothe platinum–thallium bonded cyanides. KEYWORDS:metal–metal bond, platinum, thallium,kinetics, mechanism, stopped flow, oxidative addition, cyanocomplexes, edta, redox reaction, metal cyanides, X–raydiffraction, Raman, NMR, mercury, palladium, nickel, onedimensional wire

A new family of oligonuclear cyano compounds incorporatingtransition (Pt) and main group (Tl) metals bound with anon-buttressed Pt-Tl bond was synthesised in aqueous solution.The metal-metal linkage is formed in the reaction betweenplatinum and thallium in their stable oxidation forms, Pt(II)and Tl(III), orvice versa: Pt(IV) and Tl(I). Four binuclear complexeswith a general composition [(CN)5Pt-Tl(CN)n(aq)]n-(n = 0-3) and a trinuclear species [(NC)5Pt-Tl-Pt(CN)5]3-were identified and structurally characterised insolution by multinuclear NMR, EXAFS and vibrationalspectroscopy. In aqueous solution the complexes exist inequilibrium. The distribution between the species can bealtered by varying the molar ratio Pt/Tl, cyanide concentrationand pH. Stability constants of the compounds weredetermined. A new compound (NC)5PtTl was also prepared in solid and its crystalstructure solved by a combination of X-ray powder diffractionand EXAFS. Altogether the values of195Pt-205Tl spin-spin coupling constants (25-71 kHz),interatomic Pt-Tl distances (2.598-2.638 Å), and vibrationstretching frequencies v (Pt-Tl) (159-164 cm-1) are fully indicative of a direct and unsupportedPt-Tl bond. The calculated values of Pt-Tl force constants(1.56-1.74 N· cm-1) are characteristic for single metal-metal bond.The oxidation status in the compounds can be viewed asintermediate between II and IV for platinum, and between I andIII for thallium, as reflected by the chemical shifts of195Pt and205Tl nuclei, C≡ N stretching frequencies andelectron binding energies. The compounds are capable to undergo a photoinducedtwo-electron transfer between the coupled hetero-metal ions.Upon irradiation into the metal-to-metal charge transferabsorption band, effective photoredox reaction takes place. Itresults in scission of the Pt-Tl bond and formation of variouscomplexes of oxidised platinum (Pt(III, IV)) and reducedthallium (Tl(I)). The values of photodecomposition quantumyields were determined from a stationary photolysis study ofthe heterometallic complexes. Nanosecond laser flash photolysisof the heteronuclear Pt-Tl cyano compounds was performed in thetimescale range 1· 10-6- 5· 10-2s and several intermediate species were detectedand characterised by optical spectroscopy. The heteronuclear Pt-Tl cyano compounds can be furthermodified in terms of their stability, solubility, and lightabsorption characteristics. It has been found that the platinumpentacyano unit of the [(NC)5Pt-Tl(CN)n(aq)]n-species is inert towards the tested ligands,whereas the thallium "part" of the complexes can be tunedsignificantly. A number of complexes [(NC)5Pt-Tl(L)m]x-(L-ligand) were prepared and characterised insolution. Compounds [(NC)5Pt-Tl(nta)(H2O)]3-, [(NC)5Pt-Tl(bipy)(DMSO)3], and [(NC)5Pt-Tl(bipy)2]have been prepared in solid and their structuresdetermined by single-crystal X-ray diffraction. <b>Keywords:</b>thallium, platinum, cyanide, metal-metal bond,non-buttressed, heterobimetallic, photoinduced, electrontransfer, redox reaction, NMR, chemical shift, spin-spincoupling constant, Raman, EXAFS, X-ray diffraction,equilibrium, oxidation state, oxidative addition,photolysis

<p>A new family of oligonuclear cyano compounds incorporatingtransition (Pt) and main group (Tl) metals bound with anon-buttressed Pt-Tl bond was synthesised in aqueous solution.The metal-metal linkage is formed in the reaction betweenplatinum and thallium in their stable oxidation forms, Pt(II)and Tl(III), or<i>vice versa</i>: Pt(IV) and Tl(I). Four binuclear complexeswith a general composition [(CN)₅Pt-Tl(CN)_n(aq)]^n-(n = 0-3) and a trinuclear species [(NC)₅Pt-Tl-Pt(CN)₅]^3-were identified and structurally characterised insolution by multinuclear NMR, EXAFS and vibrationalspectroscopy. In aqueous solution the complexes exist inequilibrium. The distribution between the species can bealtered by varying the molar ratio Pt/Tl, cyanide concentrationand pH. Stability constants of the compounds weredetermined.</p><p>A new compound (NC)₅PtTl was also prepared in solid and its crystalstructure solved by a combination of X-ray powder diffractionand EXAFS. Altogether the values of¹⁹⁵Pt-²⁰⁵Tl spin-spin coupling constants (25-71 kHz),interatomic Pt-Tl distances (2.598-2.638 Å), and vibrationstretching frequencies v (Pt-Tl) (159-164 cm^-1) are fully indicative of a direct and unsupportedPt-Tl bond. The calculated values of Pt-Tl force constants(1.56-1.74 N· cm^-1) are characteristic for single metal-metal bond.The oxidation status in the compounds can be viewed asintermediate between II and IV for platinum, and between I andIII for thallium, as reflected by the chemical shifts of¹⁹⁵Pt and²⁰⁵Tl nuclei, C≡ N stretching frequencies andelectron binding energies.</p><p>The compounds are capable to undergo a photoinducedtwo-electron transfer between the coupled hetero-metal ions.Upon irradiation into the metal-to-metal charge transferabsorption band, effective photoredox reaction takes place. Itresults in scission of the Pt-Tl bond and formation of variouscomplexes of oxidised platinum (Pt(III, IV)) and reducedthallium (Tl(I)). The values of photodecomposition quantumyields were determined from a stationary photolysis study ofthe heterometallic complexes. Nanosecond laser flash photolysisof the heteronuclear Pt-Tl cyano compounds was performed in thetimescale range 1· 10^-6- 5· 10^-2s and several intermediate species were detectedand characterised by optical spectroscopy.</p><p>The heteronuclear Pt-Tl cyano compounds can be furthermodified in terms of their stability, solubility, and lightabsorption characteristics. It has been found that the platinumpentacyano unit of the [(NC)₅Pt-Tl(CN)_n(aq)]^n-species is inert towards the tested ligands,whereas the thallium "part" of the complexes can be tunedsignificantly. A number of complexes [(NC)₅Pt-Tl(L)_m]^x-(L-ligand) were prepared and characterised insolution. Compounds [(NC)₅Pt-Tl(nta)(H₂O)]^3-, [(NC)₅Pt-Tl(bipy)(DMSO)₃], and [(NC)₅Pt-Tl(bipy)₂]have been prepared in solid and their structuresdetermined by single-crystal X-ray diffraction.</p><p><b>Keywords:</b>thallium, platinum, cyanide, metal-metal bond,non-buttressed, heterobimetallic, photoinduced, electrontransfer, redox reaction, NMR, chemical shift, spin-spincoupling constant, Raman, EXAFS, X-ray diffraction,equilibrium, oxidation state, oxidative addition,photolysis</p>