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- Genre: Academic theses
- Creators: Liu, Yan
- Creators: Moore, Ana L
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Description
Photosynthesis, one of the most important processes in nature, has provided an energy basis for nearly all life on Earth, as well as the fossil fuels we use today to power modern society. This research aims to mimic the photosynthetic process of converting incident solar energy into chemical potential energy in the form of a fuel via systems capable of carrying out photo-induced electron transfer to drive the production of hydrogen from water. Herein is detailed progress in using photo-induced stepwise electron transfer to drive the oxidation of water and reduction of protons to hydrogen. In the design, use of more blue absorbing porphyrin dyes to generate high-potential intermediates for oxidizing water and more red absorbing phthalocyanine dyes for forming the low potential charge needed for the production of hydrogen have been utilized. For investigating water oxidation at the photoanode, high potential porphyrins such as, bis-pyridyl porphyrins and pentafluorophenyl porphyrins have been synthesized and experiments have aimed at the co-immobilization of this dye with an IrO2-nH2O catalyst on TiO2. To drive the cathodic reaction of the water splitting photoelectrochemical cell, utilization of silicon octabutoxy-phthalocyanines have been explored, as they offer good absorption in the red to near infrared, coupled with low potential photo-excited states. Axially and peripherally substituted phthalocyanines bearing carboxylic anchoring groups for the immobilization on semiconductors such as TiO2 has been investigated. Ultimately, this work should culminate in a photoelectrochemical cell capable of splitting water to oxygen and hydrogen with the only energy input from light. A series of perylene dyes bearing multiple semi-conducting metal oxide anchoring groups have been synthesized and studied. Results have shown interfacial electron transfer between these perylenes and TiO2 nanoparticles encapsulated within reverse micelles and naked nanoparticles. The binding process was followed by monitoring the hypsochromic shift of the dye absorption spectra over time. Photoinduced electron transfer from the singlet excited state of the perylenes to the TiO2 conduction band is indicated by emission quenching of the TiO2-bound form of the dyes and confirmed by transient absorption measurements of the radical cation of the dyes and free carriers (injected electrons) in the TiO2.
ContributorsBergkamp, Jesse J (Author) / Moore, Ana L (Thesis advisor) / Mariño-Ochoa, Ernesto (Thesis advisor) / Gust, Devens J (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2013
Description
As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA nanotechnology which is the main topic of this dissertation. The ability of rationally designed DNA strands to self-assemble into arbitrary nanostructures without external direction is the basis of this field. A series of novel design principles for DNA nanotechnology are presented here, from topological DNA nanostructures to complex and curved DNA nanostructures, from pure DNA nanostructures to hybrid RNA/DNA nanostructures. As one of the most important and pioneering fields in controlling the assembly of materials (both DNA and other materials) at the nanoscale, DNA nanotechnology is developing at a dramatic speed and as more and more construction approaches are invented, exciting advances will emerge in ways that we may or may not predict.
ContributorsHan, Dongran (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Ros, Anexandra (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2012
Description
Solar energy is a promising alternative for addressing the world's current and future energy requirements in a sustainable way. Because solar irradiation is intermittent, it is necessary to store this energy in the form of a fuel so it can be used when required. The light-driven splitting of water into oxygen and hydrogen (a useful chemical fuel) is a fascinating theoretical and experimental challenge that is worth pursuing because the advance of the knowledge that it implies and the availability of water and sunlight. Inspired by natural photosynthesis and building on previous work from our laboratory, this dissertation focuses on the development of water-splitting dye-sensitized photoelectrochemical tandem cells (WSDSPETCs). The design, synthesis, and characterization of high-potential porphyrins and metal-free phthalocyanines with phosphonic anchoring groups are reported. Photocurrents measured for WSDSPETCs made with some of these dyes co-adsorbed with molecular or colloidal catalysts on TiO2 electrodes are reported as well. To guide in the design of new molecules we have used computational quantum chemistry extensively. Linear correlations between calculated frontier molecular orbital energies and redox potentials were built and tested at multiple levels of theory (from semi-empirical methods to density functional theory). Strong correlations (with r2 values > 0.99) with very good predictive abilities (rmsd < 50 mV) were found when using density functional theory (DFT) combined with a continuum solvent model. DFT was also used to aid in the elucidation of the mechanism of the thermal relaxation observed for the charge-separated state of a molecular triad that mimics the photo-induced proton coupled electron transfer of the tyrosine-histidine redox relay in the reaction center of Photosystem II. It was found that the inclusion of explicit solvent molecules, hydrogen bonded to specific sites within the molecular triad, was essential to explain the observed thermal relaxation. These results are relevant for both advancing the knowledge about natural photosynthesis and for the future design of new molecules for WSDSPETCs.
ContributorsMéndez-Hernández, Dalvin D (Author) / Moore, Ana L (Thesis advisor) / Mujica, Vladimiro (Thesis advisor) / Gust, Devens J. (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Natural photosynthesis dedicates specific proteins to achieve the modular division of the essential roles of solar energy harvesting, charge separation and carrier transport within natural photosynthesis. The modern understanding of the fundamental photochemistry by which natural photosynthesis operates is well advanced and solution state mimics of the key photochemical processes have been reported previously. All of the early events in natural photosynthesis responsible for the conversion of solar energy to electric potential energy occur within proteins and phospholipid membranes that act as scaffolds for arranging the active chromophores. Accordingly, for creating artificial photovoltaic (PV) systems, scaffolds are required to imbue structure to the systems. An approach to incorporating modular design into solid-state organic mimics of the natural system is presented together with how conductive scaffolds can be utilized in organic PV systems. To support the chromophore arrays present within this design and to extract separated charges from within the structure, linear pyrazine-containing molecular ribbons were chosen as candidates for forming conductive linear scaffolds that could be functionalized orthogonally to the linear axis. A series of donor-wire-acceptor (D-W-A) compounds employing porphyrins as the donors and a C60 fullerene adduct as the acceptors have been synthesized for studying the ability of the pyrazine-containing hetero-aromatic wires to mediate photoinduced electron transfer between the porphyrin donor and fullerene acceptor. Appropriate substitutions were made and the necessary model compounds useful for dissecting the complex photochemistry that the series is expected to display were also synthesized. A dye was synthesized using a pyrazine-containing heteroaromatic spacer that features two porphyrin chromophores. The dye dramatically outperforms the control dye featuring the same porphyrin and a simple benzoic acid linker. A novel, highly soluble 6+kDa extended phthalocyanine was also synthesized and exhibits absorption out to 900nm. The extensive functionalization of the extended phthalocyanine core with dodecyl groups enabled purification and characterization of an otherwise insoluble entity. Finally, in the interest of incorporating modular design into plastic solar cells, a series of porphyrin-containing monomers have been synthesized that are intended to form dyadic and triadic molecular-heterojunction polymers with dedicated hole and electron transport pathways during electrochemical polymerization.
ContributorsWatson, Brian Lyndon (Author) / Gust, Devens (Thesis advisor) / Gould, Ian (Committee member) / Moore, Ana L (Committee member) / Arizona State University (Publisher)
Created2013
Description
DNA is a unique, highly programmable and addressable biomolecule. Due to its reliable and predictable base recognition behavior, uniform structural properties, and extraordinary stability, DNA molecules are desirable substrates for biological computation and nanotechnology. The field of DNA computation has gained considerable attention due to the possibility of exploiting the massive parallelism that is inherent in natural systems to solve computational problems. This dissertation focuses on building novel types of computational DNA systems based on both DNA reaction networks and DNA nanotechnology. A series of related research projects are presented here. First, a novel, three-input majority logic gate based on DNA strand displacement reactions was constructed. Here, the three inputs in the majority gate have equal priority, and the output will be true if any two of the inputs are true. We subsequently designed and realized a complex, 5-input majority logic gate. By controlling two of the five inputs, the complex gate is capable of realizing every combination of OR and AND gates of the other 3 inputs. Next, we constructed a half adder, which is a basic arithmetic unit, from DNA strand operated XOR and AND gates. The aim of these two projects was to develop novel types of DNA logic gates to enrich the DNA computation toolbox, and to examine plausible ways to implement large scale DNA logic circuits. The third project utilized a two dimensional DNA origami frame shaped structure with a hollow interior where DNA hybridization seeds were selectively positioned to control the assembly of small DNA tile building blocks. The small DNA tiles were directed to fill the hollow interior of the DNA origami frame, guided through sticky end interactions at prescribed positions. This research shed light on the fundamental behavior of DNA based self-assembling systems, and provided the information necessary to build programmed nanodisplays based on the self-assembly of DNA.
ContributorsLi, Wei (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Colloidal quantum dots (QDs) or semiconductor nanocrystals are often used to describe 2 to 20 nm solution processed nanoparticles of various semiconductor materials that display quantum confinement effects. Compared to traditional fluorescent organic dyes, QDs provide many advantages. For biological applications it is necessary to develop reliable methods to functionalize QDs with hydrophilic biomolecules so that they may maintain their stability and functionality in physiological conditions. DNA, a molecule that encodes genetic information, is arguably the smartest molecule that nature has ever produced and one of the most explored bio-macromolecules. DNA directed self-assembly can potentially organize QDs that are functionalized with DNA with nanometer precision, and the resulting arrangements may facilitate the display of novel optical properties. The goal of this dissertation was to achieve a robust reliable yet simple strategy to link DNA to QDs so that they can be used for DNA directed self assembly by which we can engineer their optical properties. Presented here is a series of studies to achieve this goal. First we demonstrate the aqueous synthesis of colloidal nanocrystal heterostructures consisting of the CdTe core encapsulated by CdS/ZnS or CdSe/ZnS shells using glutathione (GSH), a tripeptide, as the capping ligand. We next employed this shell synthesis strategy to conjugate PS-PO chimeric DNA to QDs at the time of shell synthesis. We synthesized a library of DNA linked QDs emitting from UV to near IR that are very stable in high salt concentrations. These DNA functionalized QDs were further site-specifically organized on DNA origami in desired patterns directed by DNA self-assembly. We further extended our capability to functionalize DNA to real IR emitting CdxPb1-xTe alloyed QDs, and demonstrated their stability by self-assembling them on DNA origami. The photo-physical properties of the QDs were further engineered by attaching a QD and a gold nanoparticle in controlled distances on the same DNA origami, which revealed a much longer range quenching effect than usual Forster Resonance Energy Transfer. We are currently engaged in enhancing photoluminescence intensity of the QDs by bringing them in the plasmonic hot spots generated by cluster of larger plasmonic nanoparticles.
ContributorsSamanta, Anirban (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Buttry, Daniel (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
DNA nanotechnology is one of the most flourishing interdisciplinary research fields. Through the features of programmability and predictability, DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales, and more importantly, they can be used as scaffolds for organizing other nanoparticles, proteins and chemical groups. By leveraging these molecules, DNA nanostructures can be used to direct the organization of complex bio-inspired materials that may serve as smart drug delivery systems and in vitro or in vivo bio-molecular computing and diagnostic devices. In this dissertation I describe a systematic study of the thermodynamic properties of complex DNA nanostructures, including 2D and 3D DNA origami, in order to understand their assembly, stability and functionality and inform future design endeavors. It is conceivable that a more thorough understanding of DNA self-assembly can be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications. As a biocompatible nanoscale motif, the successful integration, stabilization and separation of DNA nanostructures from cells/cell lysate suggests its potential to serve as a diagnostic platform at the cellular level. Here, DNA origami was used to capture and identify multiple T cell receptor mRNA species from single cells within a mixed cell population. This demonstrates the potential of DNA nanostructure as an ideal nano scale tool for biological applications.
ContributorsWei, Xixi (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Chen, Julian (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
The first chapter reviews three decades of artificial photosynthetic research conducted by the A. Moore, T. Moore, and D. Gust research group. Several carotenoid (Car) and tetrapyrrole containing molecules were synthesized and investigated for excitation energy transfer (EET), photoregulation, and photoprotective functions. These artificial photosynthetic compounds mimicked known processes and investigated proposed mechanisms in natural systems. This research leads to a greater understanding of photosynthesis and design concepts for organic based solar energy conversion devices. The second and third chapters analyze the triplet energy transfer in carotenoid containing dyads. Transient absorption, time-resolved FTIR and resonance Raman spectra revealed that in a 4-amide linked carotenophthalocyanine dyads the Car triplet state is shared across the larger conjugated system, which is similar to protein complexes in oxygenic photosynthetic organisms. In a carotenopurpurin dyad (CarPur) a methylene ester covalent bond prevents the purpurin (Pur) from influencing the Car triplet based on the transient absorption, time-resolved FTIR and resonance Raman spectra. Thus CarPur resembles the antenna proteins from anoxygenic photosynthetic bacteria. Additional examples of carotenoporphyrin dyads further demonstrates the need for orbital overlap for ultrafast triplet energy transfer and the formations of possible intramolecular charge transfer state. The fourth chapter studies a 4-amino phenyl carotenophthalocyanine and its model compounds using high temporal resolution transient absorption spectroscopy techniques. EET from the Car second excited (S2) state to the phthalocyanine (Pc) was determined to be 37% and a coupled hot ground state (S*)/Pc excited state spectrum was observed. Excitation of the tetrapyrrole portion of the dyad did not yield any kinetic differences, but there was an S* signal during the excited states of the dyad. This demonstrates the EET and photoregulating properties of this artificial photosynthetic compound are similar to those of natural photosynthesis. The last chapter covers the synthesis of silicon Pc (SiPc) dyes and the methods for attaching them to gold nanoparticles and flat gold surfaces. SiPc attached to patterned gold surfaces had unperturbed fluorescence, however the selectivity for the gold was low, so alternative materials are under investigation to improve the dye's selectivity for the gold surface.
ContributorsWongCarter, Katherine (Author) / Moore, Ana L (Thesis advisor) / Gust, Devens (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Spider dragline silk is an outstanding biopolymer with a strength that exceeds steel by weight and a toughness greater than high-performance fibers like Kevlar. For this reason, structural and dynamic studies on the spider silk are of great importance for developing future biomaterials. The spider dragline silk comprises two silk proteins, Major ampullate Spidroin 1 and 2 (MaSp1 and 2), which are synthesized and stored in the major ampullate (MA) gland of spiders. The initial state of the silk proteins within Black Widow MA glands was probed with solution-state NMR spectroscopy. The conformation dependent chemical shifts information indicates that the silk proteins are unstructured and in random coil conformation. 15N relaxation parameters, T1, T2 and 15N-{1H} steady-state NOE were measured to probe the backbone dynamics for MA silk proteins. These measurements indicate fast sub-nanosecond timescale backbone dynamics for the repetitive core of spider MA proteins indicating that the silk proteins are unfolded, highly flexible random coils in the MA gland. The translational diffusion coefficients of the spider silk proteins within the MA gland were measured using 1H diffusion NMR at 1H sites from different amino acids. A phenomenon was observed where the measured diffusion coefficients decrease with an increase in the diffusion delay used. The mean displacement along the external magnetic field was found to be 0.35 μm and independent of the diffusion delay. The results indicate that the diffusion of silk protein was restricted due to intermolecular cross-linking with only segmental diffusion observable.
To understand how a spider converts the unfolded protein spinning dope into a highly structured and oriented in the super fiber,the effect of acidification on spider silk assembly was investigated on native spidroins from the major ampullate (MA) gland fluid excised from Latrodectus hesperus (Black Widow) spiders. The in vitro spider silk assembly kinetics were monitored as a function of pH with a 13C solid-state Magic Angle Spinning (MAS) NMR approach. The results confirm the importance of acidic pH in the spider silk self-assembly process with observation of a sigmoidal nucleation-elongation kinetic profile. The rates of nucleation and elongation and the percentage of β-sheet structure in the grown fibers depend on pH.
The secondary structure of the major ampullate silk from Peucetia viridians (Green Lynx) spiders was characterized by X-ray diffraction (XRD) and solid-state NMR spectroscopy. From XRD measurement, β-sheet nano-crystallites were observed that are highly oriented along the fiber axis with an orientational order of 0.980. Compare to the crystalline region, the amorphous region was found to be partially oriented with an orientational order of 0.887. Further, two dimensional 13C-13C through-space and through-bond solid-state NMR experiments provide structural analysis for the repetitive amino acid motifs in the silk proteins. The nano-crystallites are mainly alanine-rich β-sheet structures. The total percentage of crystalline region is determined to be 40.0±1.2 %. 18±1 % of alanine, 60±2 % glycine and 54±2 % serine are determined to be incorporated into helical conformations while 82±1 % of alanine, 40±3 % glycine and 46±2 % serine are in the β-sheet conformation.
To understand how a spider converts the unfolded protein spinning dope into a highly structured and oriented in the super fiber,the effect of acidification on spider silk assembly was investigated on native spidroins from the major ampullate (MA) gland fluid excised from Latrodectus hesperus (Black Widow) spiders. The in vitro spider silk assembly kinetics were monitored as a function of pH with a 13C solid-state Magic Angle Spinning (MAS) NMR approach. The results confirm the importance of acidic pH in the spider silk self-assembly process with observation of a sigmoidal nucleation-elongation kinetic profile. The rates of nucleation and elongation and the percentage of β-sheet structure in the grown fibers depend on pH.
The secondary structure of the major ampullate silk from Peucetia viridians (Green Lynx) spiders was characterized by X-ray diffraction (XRD) and solid-state NMR spectroscopy. From XRD measurement, β-sheet nano-crystallites were observed that are highly oriented along the fiber axis with an orientational order of 0.980. Compare to the crystalline region, the amorphous region was found to be partially oriented with an orientational order of 0.887. Further, two dimensional 13C-13C through-space and through-bond solid-state NMR experiments provide structural analysis for the repetitive amino acid motifs in the silk proteins. The nano-crystallites are mainly alanine-rich β-sheet structures. The total percentage of crystalline region is determined to be 40.0±1.2 %. 18±1 % of alanine, 60±2 % glycine and 54±2 % serine are determined to be incorporated into helical conformations while 82±1 % of alanine, 40±3 % glycine and 46±2 % serine are in the β-sheet conformation.
ContributorsXu, Dian (Author) / Yarger, Jeffery L (Thesis advisor) / Holland, Gregory P (Thesis advisor) / Wang, Xu (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2015
Description
Scientists around the world have been striving to develop artificial light-harvesting antenna model systems for energy and other light-driven biochemical applications. Among the various approaches to achieve this goal, one of the most promising is the assembly of structurally well-defined artificial light-harvesting antennas based on the principles of structural DNA nanotechnology. DNA has recently emerged as an extremely efficient material to organize molecules such as fluorophores and proteins on the nanoscale. It is desirable to develop a hybrid smart material by combining artificial antenna systems based on DNA with natural reaction center components, so that the material can be engineered to convert light energy to chemical energy via formation of a charge-separated state.
Presented here are a series of studies toward this goal. First, self-assembled seven-helix DNA bundles (7HB) with cyclic arrays of three distinct chromophores were developed. The spectral properties and energy transfer mechanisms in the artificial light-harvesting antenna were studied extensively using steady-state and time-resolved methods. Next, engineered cysteine residues in the reaction center of the purple photosynthetic bacterium Rhodobacter sphaeroides were each covalently conjugated to fluorophores in order to explore the spectral requirements for energy transfer between an artificial light harvesting system and the reaction center. Finally, a structurally well-defined and spectrally tunable artificial light-harvesting system was constructed, where multiple organic dyes were conjugated to 3-arm DNA nanostructure. A reaction center protein isolated from the purple photosynthetic bacterium Rhodobacter sphaeroides was linked to one end of the 3-arm junction to serve as the final acceptor, which converts the photonic energy absorbed by the chromophores into chemical energy by charge separation. This type of model system is required to understand how parameters such as geometry, spectral characteristics of the dyes, and conformational flexibility affect energy transfer, and can be used to inform the development of more complex model light-harvesting systems.
Presented here are a series of studies toward this goal. First, self-assembled seven-helix DNA bundles (7HB) with cyclic arrays of three distinct chromophores were developed. The spectral properties and energy transfer mechanisms in the artificial light-harvesting antenna were studied extensively using steady-state and time-resolved methods. Next, engineered cysteine residues in the reaction center of the purple photosynthetic bacterium Rhodobacter sphaeroides were each covalently conjugated to fluorophores in order to explore the spectral requirements for energy transfer between an artificial light harvesting system and the reaction center. Finally, a structurally well-defined and spectrally tunable artificial light-harvesting system was constructed, where multiple organic dyes were conjugated to 3-arm DNA nanostructure. A reaction center protein isolated from the purple photosynthetic bacterium Rhodobacter sphaeroides was linked to one end of the 3-arm junction to serve as the final acceptor, which converts the photonic energy absorbed by the chromophores into chemical energy by charge separation. This type of model system is required to understand how parameters such as geometry, spectral characteristics of the dyes, and conformational flexibility affect energy transfer, and can be used to inform the development of more complex model light-harvesting systems.
ContributorsDutta, Palash Kanti (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Chen, Julian (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014