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Description
The goal of this theoretical study of infrared spectra was to ascertain to what degree molecules may be identified from their IR spectra and which spectral regions are best suited for this purpose. The frequencies considered range from the lowest frequency molecular vibrations in the far-IR, terahertz region (below ~3 THz or 100 cm-1) up to the highest frequency vibrations (~120 THz or 4000 cm-1). An emphasis was placed on the IR spectra of chemical and biological threat molecules in the interest of detection and prevention. To calculate IR spectra, the technique of normal mode analysis was applied to organic molecules ranging in size from 8 to 11,352 atoms. The IR intensities of the vibrational modes were calculated in terms of the derivative of the molecular dipole moment with respect to each normal coordinate. Three sets of molecules were studied: the organophosphorus G- and V-type nerve agents and chemically related simulants (15 molecules ranging in size from 11 to 40 atoms); 21 other small molecules ranging in size from 8 to 24 atoms; and 13 proteins ranging in size from 304 to 11,352 atoms. Spectra for the first two sets of molecules were calculated using quantum chemistry software, the last two sets using force fields. The "middle" set used both methods, allowing for comparison between them and with experimental spectra from the NIST/EPA Gas-Phase Infrared Library. The calculated spectra of proteins, for which only force field calculations are practical, reproduced the experimentally observed amide I and II bands, but they were shifted by approximately +40 cm-1 relative to experiment. Considering the entire spectrum of protein vibrations, the most promising frequency range for differentiating between proteins was approximately 600-1300 cm-1 where water has low absorption and the proteins show some differences.
ContributorsMott, Adam J (Author) / Rez, Peter (Thesis advisor) / Ozkan, Banu (Committee member) / Shumway, John (Committee member) / Thorpe, Michael (Committee member) / Vaiana, Sara (Committee member) / Arizona State University (Publisher)
Created2012
Description
Climate change is one of the biggest challenges facing today's society.Since the late 19th century, the global average temperature has been rising. In order to minimize the temperature increase of the earth, it is necessary to develop alternative energy technologies that do not depend on fossil fuels. Solar fuels are one potential energy source for the future. Solar fuel technologies use catalysts to convert low energy molecules into fuels via artificial photosynthesis. TiO2, or titania, is an important model photocatalyst for studying these reactions. It is also important to use remaining fossil fuel resources efficiently and with the lowest possible greenhouse gas emissions. Fuel cells are electrochemical devices that aim to accomplish this goal and CeO2, or ceria, is an important material used in these devices. One way to observe the atomic structure of a material is with a transmission electron microscope (TEM). A traditional transmission electron microscope employs a beam of fast electrons to form atomic resolution images of a material. While imaging gives information about the positions of the atoms in the material, spectroscopy gives information about the composition and bonding of the material. A type of spectroscopy that can be performed inside the transmission electron microscope is electron energy loss spectroscopy (EELS), which provides a fundamental understanding of the electronic structure of a material. The energy loss spectrum also contains information on the chemical bonding in the material, and theoretical calculations that model the spectra are essential to correctly interpreting this bonding information. FEFF is a software that performs EELS calculations. Calculations of the oxygen K edges of TiO2 and CeO2 were made using FEFF in order to understand the changes that occur in the spectrum when oxygen vacancies are introduced as well as the changes near a grain boundary.
ContributorsHussaini, Zahra (Author) / Crozier, Peter (Thesis director) / Rez, Peter (Committee member) / Jorissen, Kevin (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Materials Science and Engineering Program (Contributor) / Department of Physics (Contributor)
Created2013-12
Description
This honors thesis is focused on two separate catalysis projects conducted under the mentorship of Dr. Javier Pérez-Ramírez at ETH Zürich. The first project explored ethylene oxychlorination over supported europium oxychloride catalysts. The second project investigated alkyne semihydrogenation over nickel phosphide catalysts. This work is the subject of a publication of which I am a co-author, as cited below.
Project 1 Abstract: Ethylene Oxychlorination
The current two-step process for the industrial process of vinyl chloride production involves CuCl2 catalyzed ethylene oxychlorination to ethylene dichloride followed by thermal cracking of the latter to vinyl chloride. To date, no industrial application of a one-step process is available. To close this gap, this work evaluates a wide range of self-prepared supported CeO2 and EuOCl catalysts for one-step production of vinyl chloride from ethylene in a fixed-bed reactor at 623 773 K and 1 bar using feed ratios of C2H4:HCl:O2:Ar:He = 3:3 6:1.5 6:3:82 89.5. Among all studied systems, CeO2/ZrO2 and CeO2/Zeolite MS show the highest activity but suffer from severe combustion of ethylene, forming COx, while 20 wt.% EuOCl/γ-Al2O3 leads to the best vinyl chloride selectivity of 87% at 15.6% C2H4 conversion with complete suppression of CO2 formation and only 4% selectivity to CO conversion for over 100 h on stream. Characterization by XRD and EDX mapping reveals that much of the Eu is present in non-active phases such as Al2Eu or EuAl4, indicating that alternative synthesis methods could be employed to better utilize the metal. A linear relationship between conversion and metal loading is found for this catalyst, indicating that always part of the used Eu is available as EuOCl, while the rest forms inactive europium aluminate species. Zeolite-supported EuOCl slightly outperforms EuOCl/γ Al2O3 in terms of total yield, but is prone to significant coking and is unstable. Even though a lot of Eu seems locked in inactive species on EuOCl/γ Al2O3, these results indicate possible savings of nearly 16,000 USD per kg of catalyst compared to a bulk EuOCl catalyst. These very promising findings constitute a crucial step for process intensification of polyvinyl chloride production and exploring the potential of supported EuOCl catalysts in industrially-relevant reactions.
Project 2 Abstract: Alkyne Semihydrogenation
Despite strongly suffering from poor noble metal utilization and a highly toxic selectivity modifier (Pb), the archetypal catalyst applied for the three-phase alkyne semihydrogenation, the Pb-doped Pd/CaCO3 (Lindlar catalyst), is still being utilized at industrial level. Inspired by the very recent strategies involving the modification of Pd with p-block elements (i.e., S), this work extrapolates the concept by preparing crystalline metal phosphides with controlled stoichiometry. To develop an affordable and environmentally-friendly alternative to traditional hydrogenation catalysts, nickel, a metal belonging to the same group as Pd and capable of splitting molecular hydrogen has been selected. Herein, a simple two-step synthesis procedure involving nontoxic precursors was used to synthesize bulk nickel phosphides with different stoichiometries (Ni2P, Ni5P4, and Ni12P5) by controlling the P:Ni ratios. To uncover structural and surface features, this catalyst family is characterized with an array of methods including X-ray diffraction (XRD), 31P magic-angle nuclear magnetic resonance (MAS-NMR) spectroscopy, and X-ray photoelectron spectroscopy (XPS). Bulk-sensitive techniques prove the successful preparation of pure phases while XPS analysis unravels the facile passivation occurring at the NixPy surface that persists even after reductive treatment. To assess the characteristic surface fingerprints of these materials, Ar sputtering was carried out at different penetration depths, reveling the presence of Ni+ and P-species. Continuous-flow three-phase hydrogenations of short-chain acetylenic compounds display that the oxidized layer covering the surface is reduced under reaction conditions, as evidenced by the induction period before reaching the steady state performance. To assess the impact of the phosphidation treatment on catalytic performance, the catalysts were benchmarked against a commercial Ni/SiO2-Al2O3 sample. While Ni/SiO2-Al2O3 presents very low selectivity to the alkene (the selectivity is about 10% at full conversion) attributed to the well-known tendency of naked nickel nanoparticles to form hydrides, the performance of nickel phosphides is highly selective and independent of P:Ni ratio. In line with previous findings on PdxS, kinetic tests indicate the occurrence of a dual-site mechanism where the alkyne and hydrogen do not compete for the same site.
This work is the subject of a publication of which I am a co-author, as cited below.
D. Albani; K. Karajovic; B. Tata; Q. Li; S. Mitchell; N. López; J. Pérez-Ramírez. Ensemble Design in Nickel Phosphide Catalysts for Alkyne Semi-Hydrogenation. ChemCatChem 2019. doi.org/10.1002/cctc.201801430
Project 1 Abstract: Ethylene Oxychlorination
The current two-step process for the industrial process of vinyl chloride production involves CuCl2 catalyzed ethylene oxychlorination to ethylene dichloride followed by thermal cracking of the latter to vinyl chloride. To date, no industrial application of a one-step process is available. To close this gap, this work evaluates a wide range of self-prepared supported CeO2 and EuOCl catalysts for one-step production of vinyl chloride from ethylene in a fixed-bed reactor at 623 773 K and 1 bar using feed ratios of C2H4:HCl:O2:Ar:He = 3:3 6:1.5 6:3:82 89.5. Among all studied systems, CeO2/ZrO2 and CeO2/Zeolite MS show the highest activity but suffer from severe combustion of ethylene, forming COx, while 20 wt.% EuOCl/γ-Al2O3 leads to the best vinyl chloride selectivity of 87% at 15.6% C2H4 conversion with complete suppression of CO2 formation and only 4% selectivity to CO conversion for over 100 h on stream. Characterization by XRD and EDX mapping reveals that much of the Eu is present in non-active phases such as Al2Eu or EuAl4, indicating that alternative synthesis methods could be employed to better utilize the metal. A linear relationship between conversion and metal loading is found for this catalyst, indicating that always part of the used Eu is available as EuOCl, while the rest forms inactive europium aluminate species. Zeolite-supported EuOCl slightly outperforms EuOCl/γ Al2O3 in terms of total yield, but is prone to significant coking and is unstable. Even though a lot of Eu seems locked in inactive species on EuOCl/γ Al2O3, these results indicate possible savings of nearly 16,000 USD per kg of catalyst compared to a bulk EuOCl catalyst. These very promising findings constitute a crucial step for process intensification of polyvinyl chloride production and exploring the potential of supported EuOCl catalysts in industrially-relevant reactions.
Project 2 Abstract: Alkyne Semihydrogenation
Despite strongly suffering from poor noble metal utilization and a highly toxic selectivity modifier (Pb), the archetypal catalyst applied for the three-phase alkyne semihydrogenation, the Pb-doped Pd/CaCO3 (Lindlar catalyst), is still being utilized at industrial level. Inspired by the very recent strategies involving the modification of Pd with p-block elements (i.e., S), this work extrapolates the concept by preparing crystalline metal phosphides with controlled stoichiometry. To develop an affordable and environmentally-friendly alternative to traditional hydrogenation catalysts, nickel, a metal belonging to the same group as Pd and capable of splitting molecular hydrogen has been selected. Herein, a simple two-step synthesis procedure involving nontoxic precursors was used to synthesize bulk nickel phosphides with different stoichiometries (Ni2P, Ni5P4, and Ni12P5) by controlling the P:Ni ratios. To uncover structural and surface features, this catalyst family is characterized with an array of methods including X-ray diffraction (XRD), 31P magic-angle nuclear magnetic resonance (MAS-NMR) spectroscopy, and X-ray photoelectron spectroscopy (XPS). Bulk-sensitive techniques prove the successful preparation of pure phases while XPS analysis unravels the facile passivation occurring at the NixPy surface that persists even after reductive treatment. To assess the characteristic surface fingerprints of these materials, Ar sputtering was carried out at different penetration depths, reveling the presence of Ni+ and P-species. Continuous-flow three-phase hydrogenations of short-chain acetylenic compounds display that the oxidized layer covering the surface is reduced under reaction conditions, as evidenced by the induction period before reaching the steady state performance. To assess the impact of the phosphidation treatment on catalytic performance, the catalysts were benchmarked against a commercial Ni/SiO2-Al2O3 sample. While Ni/SiO2-Al2O3 presents very low selectivity to the alkene (the selectivity is about 10% at full conversion) attributed to the well-known tendency of naked nickel nanoparticles to form hydrides, the performance of nickel phosphides is highly selective and independent of P:Ni ratio. In line with previous findings on PdxS, kinetic tests indicate the occurrence of a dual-site mechanism where the alkyne and hydrogen do not compete for the same site.
This work is the subject of a publication of which I am a co-author, as cited below.
D. Albani; K. Karajovic; B. Tata; Q. Li; S. Mitchell; N. López; J. Pérez-Ramírez. Ensemble Design in Nickel Phosphide Catalysts for Alkyne Semi-Hydrogenation. ChemCatChem 2019. doi.org/10.1002/cctc.201801430
ContributorsTata, Bharath (Author) / Deng, Shuguang (Thesis director) / Muhich, Christopher (Committee member) / Chemical Engineering Program (Contributor, Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Operando transmission electron microscopy (TEM) is an extension of in-situ TEM in which the performance of the material being observed is measured simultaneously. This is of great value, since structure-performance relationships lie at the heart of materials science. For catalyst materials, like the SiO2-supported Ru nanoparticles studied, the important performance metric, catalyst activity, is measured inside the microscope by determining the gas composition during imaging. This is accomplished by acquisition of electron energy loss spectra (EELS) of the gas in the environmental TEM while catalysis is taking place. In this work, automated methods for rapidly quantifying low-loss and core-loss EELS of gases were developed. A new sample preparation method was also established to increase catalytic conversion inside a differentially-pumped environmental TEM, and the maximum CO conversion observed was about 80%. A system for mixing gases and delivering them to the environmental TEM was designed and built, and a method for locating and imaging nanoparticles in zone axis orientations while minimizing electron dose rate was determined.
After atomic resolution images of Ru nanoparticles observed during CO oxidation were obtained, the shape and surface structures of these particles was investigated. A Wulff model structure for Ru particles was compared to experimental images both by manually rotating the model, and by automatically determining a matching orientation using cross-correlation of shape signatures. From this analysis, it was determined that most Ru particles are close to Wulff-shaped during CO oxidation. While thick oxide layers were not observed to form on Ru during CO oxidation, thin RuO2 layers on the surface of Ru nanoparticles were imaged with atomic resolution for the first time. The activity of these layers is discussed in the context of the literature on the subject, which has thus far been inconclusive. We conclude that disordered oxidized ruthenium, rather than crystalline RuO2 is the most active species.
After atomic resolution images of Ru nanoparticles observed during CO oxidation were obtained, the shape and surface structures of these particles was investigated. A Wulff model structure for Ru particles was compared to experimental images both by manually rotating the model, and by automatically determining a matching orientation using cross-correlation of shape signatures. From this analysis, it was determined that most Ru particles are close to Wulff-shaped during CO oxidation. While thick oxide layers were not observed to form on Ru during CO oxidation, thin RuO2 layers on the surface of Ru nanoparticles were imaged with atomic resolution for the first time. The activity of these layers is discussed in the context of the literature on the subject, which has thus far been inconclusive. We conclude that disordered oxidized ruthenium, rather than crystalline RuO2 is the most active species.
ContributorsMiller, Benjamin (Author) / Crozier, Peter (Thesis advisor) / Liu, Jingyue (Committee member) / McCartney, Martha (Committee member) / Rez, Peter (Committee member) / Arizona State University (Publisher)
Created2016
Description
The structure-function relation in Biology suggests that every biological molecule has evolved its structure to carry out a specific function. However, for many of these processes (such as those with catalytic activity) the structure of the biomolecule changes during the course of a reaction. Understanding the structure-function relation thus becomes a question of understanding biomolecular dynamics that span a variety of timescales (from electronic rearrangements in the femtoseconds to side-chain alteration in the microseconds and more). This dissertation deals with the study of biomolecular dynamics in the ultrafast timescales (fs-ns) using electron and X-ray probes in both time and frequency domains.
It starts with establishing the limitations of traditional electron diffraction coupled with molecular replacement to study biomolecular structure and proceeds to suggest a pulsed electron source Hollow-Cone Transmission Electron Microscope as an alternative scheme to pursue ultrafast biomolecular imaging. In frequency domain, the use of Electron Energy Loss Spectroscopy as a tool to access ultrafast nuclear dynamics in the steady state, is detailed with the new monochromated NiON UltraSTEM and examples demonstrating this instrument’s capability are provided.
Ultrafast X-ray spectroscopy as a tool to elucidate biomolecular dynamics is presented in studying X-ray as a probe, with the study of the photolysis of Methylcobalamin using time-resolved laser pump – X-ray probe absorption spectroscopy. The analysis in comparison to prior literature as well as DFT based XAS simulations offer good agreement and understanding to the steady state spectra but are so far inadequate in explaining the time-resolved data. However, the trends in the absorption simulations for the transient intermediates show a strong anisotropic dependence on the axial ligation, which would define the direction for future studies on this material to achieve a solution.
It starts with establishing the limitations of traditional electron diffraction coupled with molecular replacement to study biomolecular structure and proceeds to suggest a pulsed electron source Hollow-Cone Transmission Electron Microscope as an alternative scheme to pursue ultrafast biomolecular imaging. In frequency domain, the use of Electron Energy Loss Spectroscopy as a tool to access ultrafast nuclear dynamics in the steady state, is detailed with the new monochromated NiON UltraSTEM and examples demonstrating this instrument’s capability are provided.
Ultrafast X-ray spectroscopy as a tool to elucidate biomolecular dynamics is presented in studying X-ray as a probe, with the study of the photolysis of Methylcobalamin using time-resolved laser pump – X-ray probe absorption spectroscopy. The analysis in comparison to prior literature as well as DFT based XAS simulations offer good agreement and understanding to the steady state spectra but are so far inadequate in explaining the time-resolved data. However, the trends in the absorption simulations for the transient intermediates show a strong anisotropic dependence on the axial ligation, which would define the direction for future studies on this material to achieve a solution.
ContributorsSubramanian, Ganesh (Author) / Spence, John (Thesis advisor) / Rez, Peter (Committee member) / Alford, Terry (Committee member) / Weierstall, Uwe (Committee member) / Kirian, Richard (Committee member) / Arizona State University (Publisher)
Created2016
Description
This dissertation features a compilation of studies concerning the biophysics of multicellular systems. I explore eukaryotic systems across length scales of the cell cytoskeleton to macroscopic scales of tissues. I begin with a general overview of the natural phenomena of life and a philosophy of investigating developmental systems in biology. The topics covered throughout this dissertation require a background in eukaryotic cell physiology, viscoelasticity, and processes of embryonic tissue morphogenesis. Following a brief background on these topics, I present an overview of the Subcellular Element Model (ScEM). This is a modeling framework which allows one to compute the dynamics of large numbers of three-dimensional deformable cells in multi-cellular systems. A primary focus of the work presented here is implementing cellular function within the framework of this model to produce biologically meaningful phenotypes. In this way, it is hoped that this modeling may inform biological understanding of the underlying mechanisms which manifest into a given cell or tissue scale phenomenon. Thus, all theoretical investigations presented here are motivated by and compared to experimental observations. With the ScEM modeling framework I first explore the passive properties of viscoelastic networks. Then as a direct extension of this work, I consider the active properties of cells, which result in biological behavior and the emergence of non-trivial biological phenotypes in cells and tissues. I then explore the possible role of chemotaxis as a mechanism of orchestrating large scale tissue morphogenesis in the early embryonic stages of amniotes. Finally I discuss the cross-sectional topology of proliferating epithelial tissues. I show how the Subcellular Element Model (ScEM) is a phenomenological model of finite elements whose interactions can be calibrated to describe the viscoelastic properties of biological materials. I further show that implementing mechanisms of cytoskeletal remodeling yields cellular and tissue phenotypes that are more and more biologically realistic. Particularly I show that structural remodeling of the cell cytoskeleton is crucial for large scale cell deformations. I provide supporting evidence that a chemotactic dipole mechanism is able to orchestrate the type of large scale collective cell movement observed in the chick epiblast during gastrulation and primitive streak formation. Finally, I show that cell neighbor histograms provide a potentially unique signature measurement of tissue topology; such measurements may find use in identifying cellular level phenotypes from a single snapshot micrograph.
ContributorsSandersius, Sebastian Ambrose (Author) / Newman, Timothy J (Thesis advisor) / Rez, Peter (Committee member) / Ros, Robert (Committee member) / Sankey, Otto F. (Committee member) / Tsen, Kong-Thon (Committee member) / Arizona State University (Publisher)
Created2011