Matching Items (43)
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Description
Molecular dynamics simulations were used to study properties of water at the interface with nanometer-size solutes. We simulated nonpolar attractive Kihara cavities given by a Lennard-Jones potential shifted by a core radius. The dipolar response of the hydration layer to a uniform electric field substantially exceeds that of the bulk.

Molecular dynamics simulations were used to study properties of water at the interface with nanometer-size solutes. We simulated nonpolar attractive Kihara cavities given by a Lennard-Jones potential shifted by a core radius. The dipolar response of the hydration layer to a uniform electric field substantially exceeds that of the bulk. For strongly attractive solutes, the collective dynamics of the hydration layer become slow compared to bulk water, as the solute size is increased. The statistics of electric field fluctuations at the solute center are Gaussian and tend toward the dielectric continuum limit with increasing solute size. A dipolar probe placed at the center of the solute is sensitive neither to the polarity excess nor to the slowed dynamics of the hydration layer. A point dipole was introduced close to the solute-water interface to further study the statistics of electric field fluctuations generated by the water. For small dipole magnitudes, the free energy surface is single-welled, with approximately Gaussian statistics. When the dipole is increased, the free energy surface becomes double-welled, before landing in an excited state, characterized again by a single-welled surface. The intermediate region is fairly broad and is characterized by electrostatic fluctuations significantly in excess of the prediction of linear response. We simulated a solute having the geometry of C180 fullerene, with dipoles introduced on each carbon. For small dipole moments, the solvent response follows the results seen for a single dipole; but for larger dipole magnitudes, the fluctuations of the solute-solvent energy pass through a second maximum. The juxtaposition of the two transitions leads to an approximately cubic scaling of the chemical potential with the dipole strengh. Umbrella sampling techniques were used to generate free energy surfaces of the electric potential fluctuations at the heme iron in Cytochrome B562. The results were unfortunately inconclusive, as the ionic background was not effectively represented in the finite-size system.
ContributorsFriesen, Allan Dwayne (Author) / Matyushov, Dmitry V (Thesis advisor) / Angell, C Austen (Thesis advisor) / Beckstein, Oliver (Committee member) / Mujica, Vladimiro (Committee member) / Arizona State University (Publisher)
Created2012
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Description
This dissertation describes the work on two projects which involves measuring molecular conductance and studying their properties on the nanoscale using various Scanning Tunneling Microscopy (STM) techniques. The first molecule studied was a porphyrin-fullerene moiety known as a molecular Dyad for photovoltaic applications. This project is further divided into two

This dissertation describes the work on two projects which involves measuring molecular conductance and studying their properties on the nanoscale using various Scanning Tunneling Microscopy (STM) techniques. The first molecule studied was a porphyrin-fullerene moiety known as a molecular Dyad for photovoltaic applications. This project is further divided into two section, the first one involving the characterization of the Dyad monolayers and conductance measurement in the dark. The Dyads are designed to form charge separated states on illumination. The lifetime of the charged states have been measured efficiently but the single-molecule conductance through the molecules have yet to be characterized. The second part of the project describes the set-up of a novel sample stage which enables the study of molecular conductance under illumination. This part also describes the subsequent study of the molecule under illumination and the observation of a unique charge-separated state. It also contains the verification of the presence of this charge-separated using other characterization techniques like transient absorption spectroscopy. The second project described in the dissertation was studying and comparing the predicted rectifying nature of two molecules, identical in every way except for one stereocenter. This project describes the formation of monolayers of the molecule on gold and then studying and analyzing the current-voltage characteristics of the molecules and looking for rectification. Both the molecules proved to be rectifying, one more than the other as predicted by theoretical calculations.
ContributorsBhattacharyya, Shreya (Author) / Lindsay, Stuart (Thesis advisor) / Moore, Ana (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Structural details of phosphonic acid functionalized nanomaterials and protic ionic liquids (PILs) were characterized using nuclear magnetic resonance (NMR) spectroscopy. It is well known that ligands play a critical role in the synthesis and properties of nanomaterials. Therefore, elucidating the details of ligand-surface and ligand-ligand interactions is crucial to

Structural details of phosphonic acid functionalized nanomaterials and protic ionic liquids (PILs) were characterized using nuclear magnetic resonance (NMR) spectroscopy. It is well known that ligands play a critical role in the synthesis and properties of nanomaterials. Therefore, elucidating the details of ligand-surface and ligand-ligand interactions is crucial to understanding nanomaterial systems more completely.

In an effort to further the understanding of ligand-surface interactions, a combination of multi-nuclear (1H, 29Si, 31P) and multi-dimensional solid-state NMR techniques were utilized to characterize the phosphonic acid functionalization of fumed silica nanoparticles using methyl phosphonic acid (MPA) and phenyl phosphonic acid (PPA). Quantitative 31P MAS solid-state NMR measurements indicate that ligands favor a monodentate binding mode. Furthermore, 1H-1H single quantum-double quantum (SQ-DQ) back-to-back (BABA) 2D NMR spectra of silica functionalized with MPA and PPA indicate that the MPA and PPA are within 4.2±0.2 Å on the surface of the nanomaterial.

The ligand capping of phosphonic acid (PA) functionalized CdSe/ZnS core-shell quantum dots (QDs) was investigated with a combination of ligand exchange, solution and solid-state 31P NMR spectroscopy. In order to quantify the ligand populations on the surface of the QDs, ligand exchange facilitated by PPA resulted in the displacement of the PAs, and allowed for quantification of the free ligands using 31P liquid state NMR.

In addition to characterizing nanomaterials, the ionicity and transport properties of a series of diethylmethylamine (DEMA) based protic ionic liquids (PILs) were characterized, principally utilizing NMR. Gas phase proton affinity was shown to be a better predictor for the extent of proton transfer, and in turn the ionicity of the PIL, than using ∆pKa. Furthermore, pulsed field gradient (PFG) NMR was used to determine that the exchangeable proton diffuses with the cation or the anion based on the strength of the acid used to generate the PILs.
ContributorsDavidowski, Stephen (Author) / Yarger, Jeffery L. (Thesis advisor) / Holland, Gregory P (Thesis advisor) / Angell, Charles A. (Committee member) / Buttry, Daniel A. (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Waste heat energy conversion remains an inviting subject for research, given the renewed emphasis on energy efficiency and carbon emissions reduction. Solid-state thermoelectric devices have been widely investigated, but their practical application remains challenging because of cost and the inability to fabricate them in geometries that are easily compatible

Waste heat energy conversion remains an inviting subject for research, given the renewed emphasis on energy efficiency and carbon emissions reduction. Solid-state thermoelectric devices have been widely investigated, but their practical application remains challenging because of cost and the inability to fabricate them in geometries that are easily compatible with heat sources. An intriguing alternative to solid-state thermoelectric devices is thermogalvanic cells, which include a generally liquid electrolyte that permits the transport of ions. Thermogalvanic cells have long been known in the electrochemistry community, but have not received much attention from the thermal transport community. This is surprising given that their performance is highly dependent on controlling both thermal and mass (ionic) transport. This research will focus on a research project, which is an interdisciplinary collaboration between mechanical engineering (i.e. thermal transport) and chemistry, and is a largely experimental effort aimed at improving fundamental understanding of thermogalvanic systems. The first part will discuss how a simple utilization of natural convection within the cell doubles the maximum power output of the cell. In the second part of the research, some of the results from the previous part will be applied in a feasibility study of incorporating thermogalvanic waste heat recovery systems into automobiles. Finally, a new approach to enhance Seebeck coefficient by tuning the configurational entropy of a mixed-ligand complex formation of copper sulfate aqueous electrolytes will be presented. Ultimately, a summary of these results as well as possible future work that can be formed from these efforts is discussed.
ContributorsGunawan, Andrey (Author) / Phelan, Patrick E (Thesis advisor) / Buttry, Daniel A (Committee member) / Mujica, Vladimiro (Committee member) / Chan, Candace K. (Committee member) / Wang, Robert Y (Committee member) / Arizona State University (Publisher)
Created2015
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Description
A driving force for studies of water, alcohols, and amides is the determination of the role of hydrogen bonding. Hydrogen bonds can break and reform, consequently creating supramolecular structures. Understanding the role supramolecular structures play in the dynamics of monohydroxyl alcohols is important to understanding hydrogen bonding in more complex

A driving force for studies of water, alcohols, and amides is the determination of the role of hydrogen bonding. Hydrogen bonds can break and reform, consequently creating supramolecular structures. Understanding the role supramolecular structures play in the dynamics of monohydroxyl alcohols is important to understanding hydrogen bonding in more complex systems such as proteins. Since many monohydroxyl alcohols are good glass formers, dielectric spectroscopy in the supercooled regime is used to gather information about the dynamics of these liquids. Application of high external fields will reversibly alter the polarization responses of the material from the linear response. This results in nonlinear dielectric effects (NDE) such as field induced suppression (saturation) and enhancement of amplitudes (chemical effects) as well as shifts in the time constants toward slower (entropy) and faster (energy absorption) dynamics.

The first part of this thesis describes the nonlinear dielectric experiments on monohydroxyl alcohols, with an emphasis on the time dependence of NDEs. For the first time, time-dependent experiments on monoalcohols were done, the results showed that NDEs occur on the Debye time scale. Furthermore, physical vapor deposition (PVD) is used to modify the supramolecular structure of 4-methyl-3-heptanol. Upon deposition the film cannot form the ring like structures, which are preferred in the bulk material. The as deposited film shows an enhancement of the dielectric peak by a factor of approximately 11 when compared to the bulk material. The conversion from the as deposited material back to the near bulk material was found to occur on the Debye timescale.

The second part of this thesis focuses on the question of what is governing the field induced changes seen in the liquids studied. Here a complete set of high field experiments on highly polar propylene carbonate derivatives were performed. It was demonstrated that these materials exhibit a Debye-like peak and using a combination of Adam-Gibbs and Fröhlich’s definition of entropy, proposed by Johari [G.P. Johari, J. Chem. Phys 138, 154503 (2013)], cannot solely be used to describe a frustration of dynamics. It is important to note that although these material exhibit a Debye like peak, the behavior is much different than monoalcohols.
ContributorsYoung-Gonzales, Amanda R (Author) / Richert, Ranko (Thesis advisor) / Angell, Charles (Committee member) / Wolf, George (Committee member) / Arizona State University (Publisher)
Created2019
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Description
Signal transduction networks comprising protein-protein interactions (PPIs) mediate homeostatic, diseased, and therapeutic cellular responses. Mapping these networks has primarily focused on identifying interactors, but less is known about the interaction affinity, rates of interaction or their regulation. To better understand the extent of the annotated human interactome, I first examined

Signal transduction networks comprising protein-protein interactions (PPIs) mediate homeostatic, diseased, and therapeutic cellular responses. Mapping these networks has primarily focused on identifying interactors, but less is known about the interaction affinity, rates of interaction or their regulation. To better understand the extent of the annotated human interactome, I first examined > 2500 protein interactions within the B cell receptor (BCR) signaling pathway using a current, cutting-edge bioluminescence-based platform called “NanoBRET” that is capable of analyzing transient and stable interactions in high throughput. Eighty-three percent (83%) of the detected interactions have not been previously reported, indicating that much of the BCR pathway is still unexplored. Unfortunately, NanoBRET, as with all other high throughput methods, cannot determine binding kinetics or affinities. To address this shortcoming, I developed a hybrid platform that characterizes > 400 PPIs quantitatively and simultaneously in < 1 hour by combining the high throughput and flexible nature of nucleic programmable protein arrays (NAPPA) with the quantitative abilities of surface plasmon resonance imaging (SPRi). NAPPA-SPRi was then used to study the kinetics and affinities of > 12,000 PPIs in the BCR signaling pathway, revealing unique kinetic mechanisms that are employed by proteins, phosphorylation and activation states to regulate PPIs. In one example, activation of the GTPase RAC1 with nonhydrolyzable GTP-γS minimally affected its binding affinities with phosphorylated proteins but increased, on average, its on- and off-rates by 4 orders of magnitude for one-third of its interactions. In contrast, this phenomenon occurred with virtually all unphosphorylated proteins. The majority of the interactions (85%) were novel, sharing 40% of the same interactions as NanoBRET as well as detecting 55% more interactions than NanoBRET. In addition, I further validated four novel interactions identified by NAPPA-SPRi using SDS-PAGE migration and Western blot analyses. In one case, we have the first evidence of a direct enzyme-substrate interaction between two well-known proto-oncogenes that are abnormally regulated in > 30% of cancers, PI3K and MYC. Herein, PI3K is demonstrated to phosphorylate MYC at serine 62, a phosphosite that increases the stability of MYC. This study provides valuable insight into how PPIs, phosphorylation, and GTPase activation regulate the BCR signal transduction pathway. In addition, these methods could be applied toward understanding other signaling pathways, pathogen-host interactions, and the effect of protein mutations on protein interactions.
ContributorsPetritis, Brianne Ogata (Author) / LaBaer, Joshua (Thesis advisor) / Lake, Douglas (Committee member) / Wang, Shaopeng (Committee member) / Arizona State University (Publisher)
Created2018
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Description
New forms of carbon are being discovered at a rapid rate and prove to be on the frontier of cutting edge technology. Carbon possesses three energetically competitive forms of orbital hybridization, leading to exceptional blends of properties unseen in other materials. Fascinating properties found among carbon allotropes, such as, fullerenes,

New forms of carbon are being discovered at a rapid rate and prove to be on the frontier of cutting edge technology. Carbon possesses three energetically competitive forms of orbital hybridization, leading to exceptional blends of properties unseen in other materials. Fascinating properties found among carbon allotropes, such as, fullerenes, carbon nanotubes, and graphene have led to new and exciting advancement, with recent applications in defense, energy storage, construction, and electronics. Various combinations of extreme strength, high electrical and thermal conductivity, flexibility, and light weight have led to new durable and flexible display screens, optoelectronics, quantum computing, and strength enhancer coating. The quest for new carbon allotropes and future application persists.

Despite the advances in carbon-based technology, researchers have been limited to sp3 and sp2 hybridizations. While sp3 and sp2 hybridizations of carbon are well established and understood, the simplest sp1 hybridized carbon allotrope, carbyne, has been impossible to synthesize and remains elusive. This dissertation presents recent results in characterizing a new sp1 carbon material produced from using pulsed laser ablation in liquid (PLAL) to ablate a gold surface that is immersed in a carbon rich liquid. The PLAL technique provides access to extremely non-thermal environmental conditions where unexplored chemical reactions occur and can be explored to access the production of new materials. A combination of experimental and theoretical results suggests gold clusters can act as stabilizing agents as they react and adsorb onto the surface of one dimensional carbon chains to form a new class of materials termed “pseudocarbynes”. Data from several characterization techniques, including Raman spectroscopy, UV/VIS spectroscopy, and transmission electron microscopy (TEM), provide evidence for the existence of pseudocarbyne. This completely new material may possess outstanding properties, a trend seen among carbon allotropes, that can further scientific advancements.
ContributorsFujikado, Nancy (Author) / Sayres, Scott G (Thesis advisor) / Rege, Kaushal (Thesis advisor) / Green, Matthew D (Committee member) / Arizona State University (Publisher)
Created2018
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Description
The molecular modification of semiconductors has applications in energy

conversion and storage, including artificial photosynthesis. In nature, the active sites of

enzymes are typically earth-abundant metal centers and the protein provides a unique

three-dimensional environment for effecting catalytic transformations. Inspired by this

biological architecture, a synthetic methodology using surface-grafted polymers with

discrete chemical recognition sites

The molecular modification of semiconductors has applications in energy

conversion and storage, including artificial photosynthesis. In nature, the active sites of

enzymes are typically earth-abundant metal centers and the protein provides a unique

three-dimensional environment for effecting catalytic transformations. Inspired by this

biological architecture, a synthetic methodology using surface-grafted polymers with

discrete chemical recognition sites for assembling human-engineered catalysts in three-dimensional

environments is presented. The use of polymeric coatings to interface cobalt-containing

catalysts with semiconductors for solar fuel production is introduced in

Chapter 1. The following three chapters demonstrate the versatility of this modular

approach to interface cobalt-containing catalysts with semiconductors for solar fuel

production. The catalyst-containing coatings are characterized through a suite of

spectroscopic techniques, including ellipsometry, grazing angle attenuated total reflection

Fourier transform infrared spectroscopy (GATR-FTIR) and x-ray photoelectron (XP)

spectroscopy. It is demonstrated that the polymeric interface can be varied to control the

surface chemistry and photoelectrochemical response of gallium phosphide (GaP) (100)

electrodes by using thin-film coatings comprising surface-immobilized pyridyl or

imidazole ligands to coordinate cobaloximes, known catalysts for hydrogen evolution.

The polymer grafting chemistry and subsequent cobaloxime attachment is applicable to

both the (111)A and (111)B crystal face of the gallium phosphide (GaP) semiconductor,

providing insights into the surface connectivity of the hard/soft matter interface and

demonstrating the applicability of the UV-induced immobilization of vinyl monomers to

a range of GaP crystal indices. Finally, thin-film polypyridine surface coatings provide a

molecular interface to assemble cobalt porphyrin catalysts for hydrogen evolution onto

GaP. In all constructs, photoelectrochemical measurements confirm the hybrid

photocathode uses solar energy to power reductive fuel-forming transformations in

aqueous solutions without the use of organic acids, sacrificial chemical reductants, or

electrochemical forward biasing.
ContributorsBeiler, Anna Mary (Author) / Moore, Gary F. (Thesis advisor) / Moore, Thomas A. (Thesis advisor) / Redding, Kevin E. (Committee member) / Allen, James P. (Committee member) / Arizona State University (Publisher)
Created2018
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Description
The physiological phenomenon of sensing temperature is detected by transient

receptor (TRP) ion channels, which are pore forming proteins that reside in the

membrane bilayer. The cold and hot sensing TRP channels named TRPV1 and TRPM8

respectively, can be modulated by diverse stimuli and are finely tuned by proteins and

lipids. PIRT (phosphoinositide interacting

The physiological phenomenon of sensing temperature is detected by transient

receptor (TRP) ion channels, which are pore forming proteins that reside in the

membrane bilayer. The cold and hot sensing TRP channels named TRPV1 and TRPM8

respectively, can be modulated by diverse stimuli and are finely tuned by proteins and

lipids. PIRT (phosphoinositide interacting regulator of TRP channels) is a small

membrane protein that modifies TRPV1 responses to heat and TRPM8 responses to cold.

In this dissertation, the first direct measurements between PIRT and TRPM8 are

quantified with nuclear magnetic resonance and microscale thermophoresis. Using

Rosetta computational biology, TRPM8 is modeled with a regulatory, and functionally

essential, lipid named PIP2. Furthermore, a PIRT ligand screen identified several novel

small molecular binders for PIRT as well a protein named calmodulin. The ligand

screening results implicate PIRT in diverse physiological functions. Additionally, sparse

NMR data and state of the art Rosetta protocols were used to experimentally guide PIRT

structure predictions. Finally, the mechanism of thermosensing from the evolutionarily

conserved sensing domain of TRPV1 was investigated using NMR. The body of work

presented herein advances the understanding of thermosensing and TRP channel function

with TRP channel regulatory implications for PIRT.
ContributorsSisco, Nicholas John (Author) / Van Horn, Wade D (Thesis advisor) / Mills, Jeremy H (Committee member) / Wang, Xu (Committee member) / Yarger, Jeff L (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Transient molecules are of great importance having proposed applications in quantum science and technology and tests of fundamental physics. In the present dissertation, the transient molecules studied are SrOH, ThF, ThCl, YbF and YbOH; each having been selected because of their proposed application. Specifically, SrOH is a candidate of constructing

Transient molecules are of great importance having proposed applications in quantum science and technology and tests of fundamental physics. In the present dissertation, the transient molecules studied are SrOH, ThF, ThCl, YbF and YbOH; each having been selected because of their proposed application. Specifically, SrOH is a candidate of constructing a molecular magneto-optical trap (MOT). The simple actinide molecules, ThF and ThCl, were selected as ligand bonding model systems to gain insight into chemical processing of Spent Nuclear Fuel. The lanthanides YbF and YbOH are venues for the determination of electron electric dipole moment (eEDM) and the studies in this dissertation provide the requisite properties for those experiments.

Intense supersonic molecular beams of these transient molecules were generated via laser ablation and spectroscopically characterized using a novel medium-resolution two-dimensional (2D) spectroscopic approach, as well as high-resolution laser induced fluorescence (LIF). The 2D medium resolution approach, which was used in the studies SrOH, ThF, ThCl and YbOH, uses a multiplexing method that simultaneously records dispersed fluorescence and excitation spectra. A significant advantage of 2D-LIF imaging is that all the electronics states can be targeted to determine the electronics states and associated vibrational spacing individually. Consequently, in the 2D spectra of ThF, ThCl and YbOH, several previously unobserved band systems have been detected in one single scan. For the DF spectra of SrOH and YbOH, the determined branching ratios show that the transitions of these molecules are diagonal (i.e. Δv=0), which is essential for the proposed potential for laser cooling. In the high-resolution of YbF, ThF, ThCl and SrOH optical spectra were recorded to an accuracy of ±30 MHz, which represents an unprecedented precision of 1:10+8.

In addition to field free spectra, optical Stark and Zeeman studies were performed to determine the most fundamental magneto-and electro-static properties. Effective Hamiltonian operators were employed to analyze the recorded spectra and determine the spectroscopic parameters. This data set also establishes a contribution toward developing new computational methodologies for treating relativistic effects and electron correlation.
ContributorsNguyen, Duc Trung (Author) / Steimle, Timothy C (Thesis advisor) / Richert, Ranko (Committee member) / Chizmeshya, Andrew V.G. (Committee member) / Arizona State University (Publisher)
Created2019