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- All Subjects: Physical Chemistry
- Genre: Academic theses
- Creators: Chizmeshya, Andrew
- Creators: Buttry, Daniel A
Description
The objective of the present investigations is to experimentally determine the fundamental molecular properties of the transient metal containing pieces. The transient molecules have been generated using laser ablation production technique and detected by using laser induced fluorescence technique. Ultra-high resolution spectra of the diatomic molecules, 87SrF, 135&137BaF, YbF, HfF, and IrSi were recorded at a resolution of approximately 30 Mhz. The fine and hyperfine structure of these molecules were determined for the ground and the excited state. The optical Stark splittings of 180HfF and IrSi were recorded and analyzed to determine the permanent electric dipole moments of the ground and the excited state. An effective Hamiltonian operator, including the rotational, centrifugal distortion, spin-orbit, spin-spin, spin-rotation, Λ-doubling, magnetic hyperfine and quadrupole interactions, and Stark effect, was employed to model and analyze the recorded spectra. The electronic spectra of the triatomic molecules, TiO2 and ZrO2, were recorded using pulsed dye laser, LIF, spectrometer at a resolution of 300MHz. These molecules have C2v symmetry. The harmonic frequencies, lifetime measurements were determined. These spectra of ZrO2 and TiO2 were modeled using a normal coordinate analysis and Franck-Condon factor predictions. High resolution field-free and Stark effect spectra of ZrO2 were recorded and for future investigation.
ContributorsLe, Anh Thun (Author) / Steimle, Timothy C (Thesis advisor) / Richert, Ranko (Committee member) / Chizmeshya, Andrew (Committee member) / Arizona State University (Publisher)
Created2013
Description
This thesis describes the studies for two groups of molecules in the gas-phase: (a) copper monofluoride (CuF) and copper hydroxide (CuOH); (b) thorium monoxide (ThO) and tungsten carbide (WC). Copper-containing molecules (Group a) are selected to investigate the ionic bonding in transition metal-containing molecules because they have a relatively simple electronic state distribution due to the nearly filled 3d-orbital. ThO and WC (Group b) are in support of particle physics for the determination of electron electric dipole moment (eEDM), de, the existence of which indicates new physics beyond the Standard Model. The determination of the tiny eEDM requires large electric fields applied to the electron. The 3(Delta)1 states for heavy polar molecules were proposed [E. R. Meyer, J. L. Bohn, and M. P. Deskevich, Phys. Rev. A 73, 062108 (2006)] to determine de with the following attractive features: (1) large electric dipole moments; (2) large internal electric fields, Eeff, experienced by valence electrons; (3) nearly degenerate omega-doublets; (4) extremely small magnetic dipole moments. The H3(Delta)1 state for ThO and the X3(Delta)1 state for WC are both good candidates. Spectroscopic parameters (i.e. molecular electric and magnetic dipole moments, omega-doubling parameters, etc) are required for the 3(Delta)1 states of ThO and WC. High resolution optical spectra (linewidth ~50 MHz) of CuF, CuOH, ThO and WC were recorded field-free and in the presence of a static electric field (or magnetic field) using laser ablation source/supersonic expansion and laser induced fluorescence (LIF) detection. The spectra were modeled by a zero-field effective Hamiltonian operator and a Stark (or Zeeman) Hamiltonian operator with various molecular parameters. The determined molecular parameters are compared to theoretical predictions. The small omega-doubling parameter was well determined using the pump/probe microwave optical double resonance (PPMODR) technique with a much higher resolution (linewidth ~60 kHz) than optical spectroscopy. In addition to the above mentioned studies of the two groups of molecules, a resonance enhanced multi-photon ionization (REMPI) combined with a time-of-flight mass spectrometer (TOFMS) has been developed to identify the molecules responsible for observed LIF signals. The operation of this spectrometer has been tested by recording the mass spectrum of Ti/O2 and the REMPI spectrum for TiO using a two-color excitation scheme.
ContributorsWang, Fang (Author) / Steimle, Timothy C (Thesis advisor) / Chizmeshya, Andrew (Committee member) / Wolf, George (Committee member) / Arizona State University (Publisher)
Created2012
Description
Increasing concentrations of carbon dioxide in the atmosphere will inevitably lead to long-term changes in climate that can have serious consequences. Controlling anthropogenic emission of carbon dioxide into the atmosphere, however, represents a significant technological challenge. Various chemical approaches have been suggested, perhaps the most promising of these is based on electrochemical trapping of carbon dioxide using pyridine and derivatives. Optimization of this process requires a detailed understanding of the mechanisms of the reactions of reduced pyridines with carbon dioxide, which are not currently well known. This thesis describes a detailed mechanistic study of the nucleophilic and Bronsted basic properties of the radical anion of bipyridine as a model pyridine derivative, formed by one-electron reduction, with particular emphasis on the reactions with carbon dioxide. A time-resolved spectroscopic method was used to characterize the key intermediates and determine the kinetics of the reactions of the radical anion and its protonated radical form. Using a pulsed nanosecond laser, the bipyridine radical anion could be generated in-situ in less than 100 ns, which allows fast reactions to be monitored in real time. The bipyridine radical anion was found to be a very powerful one-electron donor, Bronsted base and nucleophile. It reacts by addition to the C=O bonds of ketones with a bimolecular rate constant around 1* 107 M-1 s-1. These are among the fastest nucleophilic additions that have been reported in literature. Temperature dependence studies demonstrate very low activation energies and large Arrhenius pre-exponential parameters, consistent with very high reactivity. The kinetics of E2 elimination, where the radical anion acts as a base, and SN2 substitution, where the radical anion acts as a nucleophile, are also characterized by large bimolecular rate constants in the range ca. 106 - 107 M-1 s-1. The pKa of the bipyridine radical anion was measured using a kinetic method and analysis of the data using a Marcus theory model for proton transfer. The bipyridine radical anion is found to have a pKa of 40±5 in DMSO. The reorganization energy for the proton transfer reaction was found to be 70±5 kJ/mol. The bipyridine radical anion was found to react very rapidly with carbon dioxide, with a bimolecular rate constant of 1* 108 M-1 s-1 and a small activation energy, whereas the protonated radical reacted with carbon dioxide with a rate constant that was too small to measure. The kinetic and thermodynamic data obtained in this work can be used to understand the mechanisms of the reactions of pyridines with carbon dioxide under reducing conditions.
ContributorsRanjan, Rajeev (Author) / Gould, Ian R (Thesis advisor) / Buttry, Daniel A (Thesis advisor) / Yarger, Jeff (Committee member) / Seo, Dong-Kyun (Committee member) / Arizona State University (Publisher)
Created2015
Description
Conformational changes in biomolecules often take place on longer timescales than are easily accessible with unbiased molecular dynamics simulations, necessitating the use of enhanced sampling techniques, such as adaptive umbrella sampling. In this technique, the conformational free energy is calculated in terms of a designated set of reaction coordinates. At the same time, estimates of this free energy are subtracted from the potential energy in order to remove free energy barriers and cause conformational changes to take place more rapidly. This dissertation presents applications of adaptive umbrella sampling to a variety of biomolecular systems. The first study investigated the effects of glycosylation in GalNAc2-MM1, an analog of glycosylated macrophage activating factor. It was found that glycosylation destabilizes the protein by increasing the solvent exposure of hydrophobic residues. The second study examined the role of bound calcium ions in promoting the isomerization of a cis peptide bond in the collagen-binding domain of Clostridium histolyticum collagenase. This study determined that the bound calcium ions reduced the barrier to the isomerization of this peptide bond as well as stabilizing the cis conformation thermodynamically, and identified some of the reasons for this. The third study represents the application of GAMUS (Gaussian mixture adaptive umbrella sampling) to on the conformational dynamics of the fluorescent dye Cy3 attached to the 5' end of DNA, and made predictions concerning the affinity of Cy3 for different base pairs, which were subsequently verified experimentally. Finally, the adaptive umbrella sampling method is extended to make use of the roll angle between adjacent base pairs as a reaction coordinate in order to examine the bending both of free DNA and of DNA bound to the archaeal protein Sac7d. It is found that when DNA bends significantly, cations from the surrounding solution congregate on the concave side, which increases the flexibility of the DNA by screening the repulsion between phosphate backbones. The flexibility of DNA on short length scales is compared to the worm-like chain model, and the contribution of cooperativity in DNA bending to protein-DNA binding is assessed.
ContributorsSpiriti, Justin Matthew (Author) / van der Vaart, Arjan (Thesis advisor) / Chizmeshya, Andrew (Thesis advisor) / Matyushov, Dmitry (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Created2011
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 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
Description
A lack of adequate energy storage technologies is arguably the greatest hindrance to a modern sustainable energy infrastructure. Chemical energy storage, in the form of batteries, is an obvious solution to the problem. Unfortunately, today’s state of the art battery technologies fail to meet the desired metrics for full scale electric grid and/or electric vehicle role out. Considerable effort from scientists and engineers has gone into the pursuit of battery chemistries theoretically capable of far outperforming leading technologies like Li-ion cells. For instance, an anode of the relatively abundant and cheap metal, magnesium, would boost the specific energy by over 4.6 times that of the current Li-ion anode (LiC6).
The work presented here explores the compatibility of magnesium electrolytes in TFSI–-based ionic liquids with a Mg anode (TFSI = bis(trifluoromethylsulfonyl)imide). Correlations are made between the Mg2+ speciation conditions in bulk solutions (as determined via Raman spectroscopy) and the corresponding electrochemical behavior of the electrolytes. It was found that by creating specific chelating conditions, with an appropriate Mg salt, the desired electrochemical behavior could be obtained, i.e. reversible electrodeposition and dissolution. Removal of TFSI– contact ion pairs from the Mg2+ solvation shell was found to be essential for reversible electrodeposition. Ionic liquids with polyethylene glycol chains pendent from a parent pyrrolidinium cation were synthesized and used to create the necessary complexes with Mg2+, from Mg(BH4)2, so that reversible electrodeposition from a purely ionic liquid medium was achieved.
The following document discusses findings from several electrochemical experiments on magnesium electrolytes in ionic liquids. Explanations for the failure of many of these systems to produce reversible Mg electrodeposition are provided. The key characteristics of ionic liquid systems that are capable of achieving reversible Mg electrodeposition are also given.
The work presented here explores the compatibility of magnesium electrolytes in TFSI–-based ionic liquids with a Mg anode (TFSI = bis(trifluoromethylsulfonyl)imide). Correlations are made between the Mg2+ speciation conditions in bulk solutions (as determined via Raman spectroscopy) and the corresponding electrochemical behavior of the electrolytes. It was found that by creating specific chelating conditions, with an appropriate Mg salt, the desired electrochemical behavior could be obtained, i.e. reversible electrodeposition and dissolution. Removal of TFSI– contact ion pairs from the Mg2+ solvation shell was found to be essential for reversible electrodeposition. Ionic liquids with polyethylene glycol chains pendent from a parent pyrrolidinium cation were synthesized and used to create the necessary complexes with Mg2+, from Mg(BH4)2, so that reversible electrodeposition from a purely ionic liquid medium was achieved.
The following document discusses findings from several electrochemical experiments on magnesium electrolytes in ionic liquids. Explanations for the failure of many of these systems to produce reversible Mg electrodeposition are provided. The key characteristics of ionic liquid systems that are capable of achieving reversible Mg electrodeposition are also given.
ContributorsWatkins, Tylan Strike (Author) / Buttry, Daniel A (Thesis advisor) / Wolf, George (Committee member) / Williams, Peter (Committee member) / Arizona State University (Publisher)
Created2016
Description
This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano- junctions between molecular electronic devices and biological systems.
This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junc- tion significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction.
In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH···O, OH···O, and NH···N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has fo- cused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance de- scriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular descrip- tion of conductance that is not based on the conventional view of molecular orbitals as transport channels. My findings suggest that the hydrogen-bond networks are crucial in understanding the conductance of these junctions.
A broader impact of this work pertains the fact that characterizing transport through hydrogen bonding networks may help in developing faster and cost-effective approaches to personalized medicine, to advance DNA sequencing and implantable electronics, and to progress in the design and application of new drugs.
This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junc- tion significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction.
In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH···O, OH···O, and NH···N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has fo- cused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance de- scriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular descrip- tion of conductance that is not based on the conventional view of molecular orbitals as transport channels. My findings suggest that the hydrogen-bond networks are crucial in understanding the conductance of these junctions.
A broader impact of this work pertains the fact that characterizing transport through hydrogen bonding networks may help in developing faster and cost-effective approaches to personalized medicine, to advance DNA sequencing and implantable electronics, and to progress in the design and application of new drugs.
ContributorsWimmer, Michael (Author) / Mujica, Vladimiro (Thesis advisor) / Wolf, George (Committee member) / Chizmeshya, Andrew (Committee member) / Arizona State University (Publisher)
Created2017
Description
Nanomaterials have attracted considerable attention in recent research due to their wide applications in various fields such as material science, physical science, electrical engineering, and biomedical engineering. Researchers have developed many methods for synthesizing different types of nanostructures and have further applied them in various applications. However, in many cases, a molecular level understanding of nanoparticles and their associated surface chemistry is lacking investigation. Understanding the surface chemistry of nanomaterials is of great significance for obtaining a better understanding of the properties and functions of the nanomaterials. Nuclear magnetic resonance (NMR) spectroscopy can provide a familiar means of looking at the molecular structure of molecules bound to surfaces of nanomaterials as well as a method to determine the size of nanoparticles in solution. Here, a combination of NMR spectroscopic techniques including one- and two-dimensional NMR spectroscopies was used to investigate the surface chemistry and physical properties of some common nanomaterials, including for example, thiol-protected gold nanostructures and biomolecule-capped silica nanoparticles.
Silk is a natural protein fiber that features unique properties such as excellent mechanical properties, biocompatibility, and non-linear optical properties. These appealing physical properties originate from the silk structure, and therefore, the structural analysis of silk is of great importance for revealing the mystery of these impressive properties and developing novel silk-based biomaterials as well. Here, solid-state NMR spectroscopy was used to elucidate the secondary structure of silk proteins in N. clavipes spider dragline silk and B. mori silkworm silk. It is found that the Gly-Gly-X (X=Leu, Tyr, Gln) motif in spider dragline silk is not in a β-sheet or α-helix structure and is very likely to be present in a disordered structure with evidence for 31-helix confirmation. In addition, the conformations of the Ala, Ser, and Tyr residues in silk fibroin of B. mori were investigated and it indicates that the Ala, Ser, and Tyr residues are all present in disordered structures in silk I (before spinning), while show different conformations in silk II (after spinning). Specifically, in silk II, the Ala and Tyr residues are present in both disordered structures and β-sheet structures, and the Ser residues are present primarily in β-sheet structures.
Silk is a natural protein fiber that features unique properties such as excellent mechanical properties, biocompatibility, and non-linear optical properties. These appealing physical properties originate from the silk structure, and therefore, the structural analysis of silk is of great importance for revealing the mystery of these impressive properties and developing novel silk-based biomaterials as well. Here, solid-state NMR spectroscopy was used to elucidate the secondary structure of silk proteins in N. clavipes spider dragline silk and B. mori silkworm silk. It is found that the Gly-Gly-X (X=Leu, Tyr, Gln) motif in spider dragline silk is not in a β-sheet or α-helix structure and is very likely to be present in a disordered structure with evidence for 31-helix confirmation. In addition, the conformations of the Ala, Ser, and Tyr residues in silk fibroin of B. mori were investigated and it indicates that the Ala, Ser, and Tyr residues are all present in disordered structures in silk I (before spinning), while show different conformations in silk II (after spinning). Specifically, in silk II, the Ala and Tyr residues are present in both disordered structures and β-sheet structures, and the Ser residues are present primarily in β-sheet structures.
ContributorsGuo, Chengchen (Author) / Yarger, Jeffery L (Thesis advisor) / Holland, Gregory P (Thesis advisor) / Buttry, Daniel A (Committee member) / Wang, Xu (Committee member) / Arizona State University (Publisher)
Created2017
Description
As the simplest carboxylic acid, formic acid (FA) is ubiquitous to Earth’s atmosphere, helping seed cloud nucleation and leading to acid rain. By studying the interactions between FA and high intensity light under high vacuum, conditions similar to the upper atmosphere, on other planets (either in the solar system or beyond), and even in interstellar media are emulated. These results were produced from a home built vacuum chamber system, with a Wiley-McLaren time of flight mass spectrometer and using femtosecond (fs) laser pulses. The laser characteristics were as follows: a pulse width >35 fs, center wavelength of 400 nm (probe pulse was 800 nm for the pump-probe investigation), and laser intensities at ~1015 W/cm2.At high laser intensities, the first direct experimental evidence of CO3+ was recorded from the Coulomb explosion (CE) of the formic acid dimer (FAD) from a molecular beam. Theoretical calculations provided further evidence for the formation of CO3+ from the vertical ionization of FAD. When (FA)n(H2O)mH+ clusters (n = 1-7 and m = 0-1) were exposed to similar laser intensities, the larger clusters (n = 5-7) favored complete atomization from CE, indicating that the repulsive forces within the clusters at those sizes was too great to withstand to form CO3+. The protonated nature of the clusters and the peak shapes recorded in the mass spectra suggested that neutral (FA)n+ clusters undergo a dissociation mechanism within the extraction region. A novel technique was created to calculate these dissociation times on the order of 100s of nanoseconds (ns), increasing by ~10 ns for each additional FA molecule. Using pump-probe spectroscopy, it was observed similarly that neutral (FA)n clusters with n > 1, showed evidence of ion pair formation of the form [(FA)nH+·OOCH-] on the sub-picosecond timescale, increasing by 70 fs per FA molecule. Both trends indicate that the neutral clusters prefer to form compact 3d structures, but after photoexcitation the clusters have competing pathways to ionization, either through multiphoton ionization (ns dynamics) or ion pair formation (fs dynamics) that inevitably lead to the expansion and subsequent rearrangement into linear chains for the protonated cluster.
ContributorsSutton, Shaun (Author) / Sayres, Scott G. (Thesis advisor) / Richert, Ranko (Committee member) / Chizmeshya, Andrew (Committee member) / Arizona State University (Publisher)
Created2023