Matching Items (17)
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- All Subjects: Chemistry
- Genre: Doctoral Dissertation
- Creators: Ghirlanda, Giovanna
Description
The utilization of solar energy requires an efficient means of its storage as fuel. In bio-inspired artificial photosynthesis, light energy can be used to drive water oxidation, but catalysts that produce molecular oxygen from water are required. This dissertation demonstrates a novel complex utilizing earth-abundant Ni in combination with glycine as an efficient catalyst with a modest overpotential of 0.475 ± 0.005 V for a current density of 1 mA/cm2 at pH 11. The production of molecular oxygen at a high potential was verified by measurement of the change in oxygen concentration, yielding a Faradaic efficiency of 60 ± 5%. This Ni species can achieve a current density of 4 mA/cm2 that persists for at least 10 hours. Based upon the observed pH dependence of the current amplitude and oxidation/reduction peaks, the catalysis is an electron-proton coupled process. In addition, to investigate the binding of divalent metals to proteins, four peptides were designed and synthesized with carboxylate and histidine ligands. The binding of the metals was characterized by monitoring the metal-induced changes in circular dichroism spectra. Cyclic voltammetry demonstrated that bound copper underwent a Cu(I)/Cu(II) oxidation/reduction change at a potential of approximately 0.32 V in a quasi-reversible process. The relative binding affinity of Mn(II), Fe(II), Co(II), Ni(II) and Cu(II) to the peptides is correlated with the stability constants of the Irving-Williams series for divalent metal ions. A potential application of these complexes of transition metals with amino acids or peptides is in the development of artificial photosynthetic cells.
ContributorsWang, Dong (Author) / Allen, James P. (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Redding, Kevin (Committee member) / Arizona State University (Publisher)
Created2014
Description
Natural hydrogenases catalyze the reduction of protons to molecular hydrogen reversibly under mild conditions; these enzymes have an unusual active site architecture, in which a diiron site is connected to a cubane type [4Fe-4S] cluster. Due to the relevance of this reaction to energy production, and in particular to sustainable fuel production, there have been substantial amount of research focused on developing biomimetic organometallic models. However, most of these organometallic complexes cannot revisit the structural and functional fine-tuning provided by the protein matrix as seen in the natural enzyme. The goal of this thesis is to build a protein based functional mimic of [Fe-Fe] hydrogenases. I used a 'retrosynthetic' approach that separates out two functional aspects of the natural enzyme. First, I built an artificial electron transfer domain by engineering two [4Fe-4S] cluster binding sites into an existing protein, DSD, which is a de novo designed domain swapped dimer. The resulting protein, DSD-bis[4Fe-4S], contains two clusters at a distance of 36 Å . I then varied distance between two clusters using vertical translation along the axis of the coiled coil; the resulting protein demonstrates efficient electron transfer to/from redox sites. Second, I built simple, functional artificial hydrogenases by using an artificial amino acid comprising a 1,3 dithiol moiety to anchor a biomimetic [Fe-Fe] active site within the protein scaffold Correct incorporation of the cluster into a model helical peptide was verified by UV-Vis, FTIR, ESI-MS and CD spectroscopy. This synthetic strategy is extended to the de novo design of more complex protein architectures, four-helix bundles that host the di-iron cluster within the hydrophobic core. In a separate approach, I developed a generalizable strategy to introduce organometallic catalytic sites into a protein scaffold. I introduced a biomimetic organometallic complex for proton reduction by covalent conjugation to biotin. The streptavidin-bound complex is significantly more efficient in photocatalytic hydrogen production than the catalyst alone. With these artificial proteins, it will be possible to explore the effect of second sphere interactions on the activity of the diiron center, and to include in the design properties such as compatibility with conductive materials and electrodes.
ContributorsRoy, Anindya (Author) / Ghirlanda, Giovanna (Thesis advisor) / Yan, Hao (Committee member) / Gust, Devens (Committee member) / Arizona State University (Publisher)
Created2014
Description
Atomic force microscopy (AFM) has become an important tool to characterize and image surfaces with nanoscale resolution. AFM imaging technique has been utilized to study a wide range of substances such as DNA, proteins, cells, silicon surfaces, nanowires etc. Hence AFM has become extremely important in the field of biochemistry, cell biology and material science. Functionalizing the AFM tip made it possible to detect molecules and their interaction using recognition imaging at single molecule level. Also the unbinding force of two molecules can be investigated based on AFM based single molecule force spectroscopy.
In the first study, a new chemical approach to functionalize the AFM tip in a simple and user-friendly way has been described. Copper-free click chemistry and a vinyl sulfone PEG linker have been utilized during the process. Using this technique, human thrombin and integrin were detected in separate experiments. Then a novel tri-arm linker with two recognition molecules on it was designed and two proteins (human thrombin and integrin) were detected simultaneously in the same experiment using recognition imaging. This technique can be applied to understand many multivalent interactions taking place in nature. Using the same tri-arm linker functionalized with two biotin molecules, the interaction of streptavidin with mono-biotin and bis-biotin ligands were investigated. The thermal stability of streptavidin-biotin complex was also studied using SDS-PAGE analysis.
In the final study, structure of native chromatin extracted from normal and cancer cell lines were analyzed using AFM imaging and agarose gel electrophoresis. Different salt fractions were used to extract chromatin region depending on their solubility. Mnase sensitivity of the chromatin sample was used to understand the open and closed structures of chromatin from different sources. The amount of chromatin in different salt fractions could act as an indicator of amount of open and condensed chromatin in normal and cancer cells. Eventually this ratio of closed and open structure of chromatin could be an indicator of tumorigenic nature of particular cell lines.
In the first study, a new chemical approach to functionalize the AFM tip in a simple and user-friendly way has been described. Copper-free click chemistry and a vinyl sulfone PEG linker have been utilized during the process. Using this technique, human thrombin and integrin were detected in separate experiments. Then a novel tri-arm linker with two recognition molecules on it was designed and two proteins (human thrombin and integrin) were detected simultaneously in the same experiment using recognition imaging. This technique can be applied to understand many multivalent interactions taking place in nature. Using the same tri-arm linker functionalized with two biotin molecules, the interaction of streptavidin with mono-biotin and bis-biotin ligands were investigated. The thermal stability of streptavidin-biotin complex was also studied using SDS-PAGE analysis.
In the final study, structure of native chromatin extracted from normal and cancer cell lines were analyzed using AFM imaging and agarose gel electrophoresis. Different salt fractions were used to extract chromatin region depending on their solubility. Mnase sensitivity of the chromatin sample was used to understand the open and closed structures of chromatin from different sources. The amount of chromatin in different salt fractions could act as an indicator of amount of open and condensed chromatin in normal and cancer cells. Eventually this ratio of closed and open structure of chromatin could be an indicator of tumorigenic nature of particular cell lines.
ContributorsSenapati, Subhadip (Author) / Lindsay, Stuart (Thesis advisor) / Zhang, Peiming (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2015
Description
A vast amount of energy emanates from the sun, and at the distance of Earth, approximately 172,500 TW reaches the atmosphere. Of that, 80,600 TW reaches the surface with 15,600 TW falling on land. Photosynthesis converts 156 TW in the form of biomass, which represents all food/fuel for the biosphere with about 20 TW of the total product used by humans. Additionally, our society uses approximately 20 more TW of energy from ancient photosynthetic products i.e. fossil fuels. In order to mitigate climate problems, the carbon dioxide must be removed from the human energy usage by replacement or recycling as an energy carrier. Proposals have been made to process biomass into biofuels; this work demonstrates that current efficiencies of natural photosynthesis are inadequate for this purpose, the effects of fossil fuel replacement with biofuels is ecologically irresponsible, and new technologies are required to operate at sufficient efficiencies to utilize artificial solar-to-fuels systems. Herein a hybrid bioderived self-assembling hydrogen-evolving nanoparticle consisting of photosystem I (PSI) and platinum nanoclusters is demonstrated to operate with an overall efficiency of 6%, which exceeds that of land plants by more than an order of magnitude. The system was limited by the rate of electron donation to photooxidized PSI. Further work investigated the interactions of natural donor acceptor pairs of cytochrome c6 and PSI for the thermophilic cyanobacteria Thermosynechococcus elogantus BP1 and the red alga Galderia sulphuraria. The cyanobacterial system is typified by collisional control while the algal system demonstrates a population of prebound PSI-cytochrome c6 complexes with faster electron transfer rates. Combining the stability of cyanobacterial PSI and kinetics of the algal PSI:cytochrome would result in more efficient solar-to-fuel conversion. A second priority is the replacement of platinum with chemically abundant catalysts. In this work, protein scaffolds are employed using host-guest strategies to increase the stability of proton reduction catalysts and enhance the turnover number without the oxygen sensitivity of hydrogenases. Finally, design of unnatural electron transfer proteins are explored and may introduce a bioorthogonal method of introducing alternative electron transfer pathways in vitro or in vivo in the case of engineered photosynthetic organisms.
ContributorsVaughn, Michael David (Author) / Moore, Thomas (Thesis advisor) / Fromme, Petra (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Redding, Kevin (Committee member) / Arizona State University (Publisher)
Created2014
Description
The AAA+ ATPase Rubisco activase (Rca) regulates the activity of Rubisco, the photosynthetic enzyme responsible for catalyzing biological carbon fixation. However, the detailed mechanism by which Rca self-association controls Rubisco reactivation activity remains poorly understood. In this work, we are using fluorescence correlation spectroscopy (FCS) to better characterize the thermodynamics of the assembly process of cotton Rca. We present FCS data for Rca in the presence of Mg*ATPgS and Mg*ADP and for the D173N Walker B motif mutant in the presence of Mg*ATP. Our data are consistent with promotion and stabilization of hexamers by Mg*ATPgS and Mg*ATP, whereas Mg*ADP facilitates continuous assembly. We find that in the presence of Mg·ADP, Rca self-associates in a step-wise fashion to form oligomeric and higher order forms, with a strong size dependence on subunit concentration. The monomer is the dominant species below 0.5 micromolar, whereas the hexamer appears to be most populated in the 10-30 micromolar range. Large assemblies containing on the order of 24 subunits become dominant above 40 micromolar, with continued assembly at even higher concentrations. Our data are consistent with a highly dynamic exchange of subunits among oligomeric species of diverse sizes. The most likely ADP-mediated assembly mechanism seems to involve the formation of spiral supra-molecular structures that grow along the helical axis by the step-wise addition of dimeric units. To examine the effect of Mg·ATP on oligomerization, we have generated the D173N mutant of Rca, which binds but does not hydrolyze ATP. In range of 8 and 70 micromolar, 60-80% of Rca is predicted to form hexamers in the presence of Mg*ATP compared to just 30-40% with Mg*ADP. We see a clear trend at which hexamerization occurs at high ATP:ADP ratios and in addition, at increasing concentrations of free magnesium ions to 5 milimolar that results in formation of six subunits. We present an assembly model where Mg*ATP promotes and stabilizes hexamerization at low micromolar Rca concentrations relative to Mg*ADP, and suggest that this results from closed ring hexamer formation in Mg*ATP and open hexameric spiral formation in Mg*ADP .
ContributorsKuriata, Agnieszka (Author) / Wachter, Rebekka (Thesis advisor) / Redding, Kevin (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2014
Description
Mechanisms for oxygen reduction are proposed for three distinct cases covering two ionic liquids of fundamentally different archetypes and almost thirty orders of magnitude of proton activity. Proton activity is treated both extrinsically by varying the concentration and intrinsically by selecting proton donors with a wide range of aqueous pKa values. The mechanism of oxygen reduction in ionic liquids is introduced by way of the protic ionic liquid (pIL) triethylammonium triflate (TEATf) which shares some similarities with aqueous acid solutions. Oxygen reduction in TEATf begins as the one electron rate limited step to form superoxide, O2*-, which is then rapidly protonated by the pIL cation forming the perhydroxyl radical, HO2*. The perhydroxyl radical is further reduced to peroxidate (HO2-) and hydrogen peroxide in proportions in accordance with their pKa. The reaction does not proceed beyond this point due to the adsorption of the conjugate base triethylammine interfering with the disproportionation of hydrogen peroxide. This work demonstrates that this mechanism is consistent across Pt, Au, Pd, and Ag electrodes. Two related sets of experiments were performed in the inherently aprotic ionic liquid 1-butyl-2,3-dimethylimidazolium triflate (C4dMImTf). The first involved the titration of acidic species of varying aqueous pKa into the IL while monitoring the extent of oxygen reduction as a function of pKa and potential on Pt and glassy carbon (GC) electrodes. These experiments confirmed the greater propensity of Pt to reduce oxygen by its immediate and abrupt transition from one electron reduction to four electron reduction, while oxygen reduction on GC gradually approaches four electron reduction as the potentials were driven more cathodic. The potential at which oxygen reduction initiates shows general agreement with the Nernst equation and the acid's tabulated aqueous pKa value, however at the extremely acidic end, a small deviation is observed. The second set of experiments in C4dMImTf solicited water as the proton donor for oxygen reduction in an approximation of the aqueous alkaline case. The water content was varied between extremely dry (<0.1 mol% H2O) and saturated (approximately 15.8 mol% H2O}). As the water content increased so too did the extent of oxygen reduction eventually approach two electrons on both Pt and GC. However, additional water led to a linear increase in the Tafel slope under enhanced mass transport conditions up to the point of 10 mol% water. This inhibition of oxygen adsorption is the result of the interaction between superoxide and water and more specifically is proposed to be associated with decomposition of theC4dMIm+ cation by hydroxide at the elevated temperatures required for the experiment. Oxygen reduction on both Pt and GC follows Nernstian behavior as the water content is increased. Separate mechanisms for oxygen reduction on Pt and GC are proposed based on the nature of the Nernstian response in these systems.
ContributorsZeller, Robert August (Author) / Friesen, Cody (Thesis advisor) / Sieradzki, Karl (Committee member) / Buttry, Daniel (Committee member) / Arizona State University (Publisher)
Created2011
Description
The electrode-electrolyte interface in electrochemical environments involves the understanding of complex processes relevant for all electrochemical applications. Some of these processes include electronic structure, charge storage, charge transfer, solvent dynamics and structure and surface adsorption. In order to engineer electrochemical systems, no matter the function, requires fundamental intuition of all the processes at the interface. The following work presents different systems in which the electrode-electrolyte interface is highly important. The first is a charge storage electrode utilizing percolation theory to develop an electrode architecture producing high capacities. This is followed by Zn deposition in an ionic liquid in which the deposition morphology is highly dependant on the charge transfer and surface adsorption at the interface. Electrode Architecture: A three-dimensional manganese oxide supercapacitor electrode architecture is synthesized by leveraging percolation theory to develop a hierarchically designed tri-continuous percolated network. The three percolated phases include a faradaically-active material, electrically conductive material and pore-former templated void space. The micropores create pathways for ionic conductivity, while the nanoscale electrically conducting phase provides both bulk conductivity and local electron transfer with the electrochemically active phase. Zn Electrodeposition: Zn redox in air and water stable N-ethyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, [C2nmm][NTf2] is presented. Under various conditions, characterization of overpotential, kinetics and diffusion of Zn species and morphological evolution as a function of overpotential and Zn concentration are analyzed. The surface stress evolution during Zn deposition is examined where grain size and texturing play significant rolls in compressive stress generation. Morphological repeatability in the ILs led to a novel study of purity in ionic liquids where it is found that surface adsorption of residual amine and chloride from the organic synthesis affect growth characteristics. The drivers of this work are to understand the processes occurring at the electrode-electrolyte interface and with that knowledge, engineer systems yielding optimal performance. With this in mind, the design of a bulk supercapacitor electrode architecture with excellent composite specific capacitances, as well as develop conditions producing ideal Zn deposition morphologies was completed.
ContributorsEngstrom, Erika (Author) / Friesen, Cody (Thesis advisor) / Buttry, Daniel (Committee member) / Sieradzki, Karl (Committee member) / Arizona State University (Publisher)
Created2011
Description
This work investigates in-situ stress evolution of interfacial and bulk processes in electrochemical systems, and is divided into two projects. The first project examines the electrocapillarity of clean and CO-covered electrodes. It also investigates surface stress evolution during electro-oxidation of CO at Pt{111}, Ru/Pt{111} and Ru{0001} electrodes. The second project explores the evolution of bulk stress that occurs during intercalation (extraction) of lithium (Li) and formation of a solid electrolyte interphase during electrochemical reduction (oxidation) of Li at graphitic electrodes. Electrocapillarity measurements have shown that hydrogen and hydroxide adsorption are compressive on Pt{111}, Ru/Pt{111}, and Ru{0001}. The adsorption-induced surface stresses correlate strongly with adsorption charge. Electrocatalytic oxidation of CO on Pt{111} and Ru/Pt{111} gives a tensile surface stress. A numerical method was developed to separate both current and stress into background and active components. Applying this model to the CO oxidation signal on Ru{0001} gives a tensile surface stress and elucidates the rate limiting steps on all three electrodes. The enhanced catalysis of Ru/Pt{111} is confirmed to be bi-functional in nature: Ru provides adsorbed hydroxide to Pt allowing for rapid CO oxidation. The majority of Li-ion batteries have anodes consisting of graphite particles with polyvinylidene fluoride (PVDF) as binder. Intercalation of Li into graphite occurs in stages and produces anisotropic strains. As batteries have a fixed size and shape these strains are converted into mechanical stresses. Conventionally staging phenomena has been observed with X-ray diffraction and collaborated electrochemically with the potential. Work herein shows that staging is also clearly observed in stress. The Li staging potentials as measured by differential chronopotentiometry and stress are nearly identical. Relative peak heights of Li staging, as measured by these two techniques, are similar during reduction, but differ during oxidation due to non-linear stress relaxation phenomena. This stress relaxation appears to be due to homogenization of Li within graphite particles rather than viscous flow of the binder. The first Li reduction wave occurs simultaneously with formation of a passivating layer known as the solid electrolyte interphase (SEI). Preliminary experiments have shown the stress of SEI formation to be tensile (~+1.5 MPa).
ContributorsMickelson, Lawrence (Author) / Friesen, Cody (Thesis advisor) / Sieradzki, Karl (Committee member) / Buttry, Daniel (Committee member) / Venables, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors of DNA and RNA. Threose nucleic acid (TNA) is capable of forming stable helical structures with complementary strands of itself and RNA. This provides a plausible mechanism for genetic information transfer between TNA and RNA. Therefore TNA has been proposed as a potential RNA progenitor. Using molecular evolution, functional sequences were isolated from a pool of random TNA molecules. This implicates a possible chemical framework capable of crosstalk between TNA and RNA. Further, this shows that heredity and evolution are not limited to the natural genetic system based on ribofuranosyl nucleic acids. Another alternative genetic system, glycerol nucleic acid (GNA) undergoes intrasystem pairing with superior thermalstability compared to that of DNA. Inspired by this property, I demonstrated a minimal nanostructure composed of both left- and right-handed mirro image GNA. This work suggested that GNA could be useful as promising orthogonal material in structural DNA nanotechnology.
ContributorsZhang, Su (Author) / Chaut, John C (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011
Description
Hydrogenases, the enzymes that reversibly convert protons and electrons to hydrogen, are used in all three domains of life. [NiFe]-hydrogenases are considered best suited for biotechnological applications because of their reversible inactivation with oxygen. Phylogenetically, there are four groups of [NiFe]-hydrogenases. The best characterized group, "uptake" hydrogenases, are membrane-bound and catalyze hydrogen oxidation in vivo. In contrast, the group 3 [NiFe]-hydrogenases are heteromultimeric, bifunctional enzymes that fulfill various cellular roles. In this dissertation, protein film electrochemistry (PFE) is used to characterize the catalytic properties of two group 3 [NiFe]-hydrogenases: HoxEFUYH from Synechocystsis sp. PCC 6803 and SHI from Pyrococcus furiosus. First, HoxEFUYH is shown to be biased towards hydrogen production. Upon exposure to oxygen, HoxEFUYH inactivates to two states, both of which can be reactivated on the timescale of seconds. Second, we show that PfSHI is the first example of an oxygen tolerant [NiFe]-hydrogenase that produces two inactive states upon exposure to oxygen. Both inactive states are analogous to those characterized for HoxEFUYH, but oxygen exposed PfSHI produces a greater fraction that reactivates at high potentials, enabling hydrogen oxidation in the presence of oxygen. Third, it is shown that removing the NAD(P)-reducing subunits from PfSHI leads to a decrease in bias towards hydrogen oxidation and renders the enzyme oxygen sensitive. Both traits are likely due to impaired intramolecular electron transfer. Mechanistic hypotheseses for these functional differences are considered.
ContributorsMcIntosh, Chelsea Lee (Author) / Jones, Anne K (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Buttry, Daniel (Committee member) / Arizona State University (Publisher)
Created2012