Physical Sciences and Mathematics Commons^™

Ultraviolet And Infrared Spectroscopy Of Synthetic Foldamers, Aib Homopeptides, And Solvated 1,2-Diphenylethane In The Gas Phase, Joseph R. Gord

Open Access Dissertations

The work presented here implements a supersonic jet expansion source to funnel the population of model peptides and solvated-bichromophore clusters into their low lying structural minima and to collisionally cool these minima to their respective zero-point vibrational levels. Single-conformation ultraviolet and infrared spectroscopy techniques are then used to probe these systems and investigate their electronic properties and uncover their intrinsic conformational preferences in the gas phase.

Model β/γ-peptides known as synthetic foldamers and aminoisobutyric acid (Aib) homopeptides incorporate structural constraints that are designed/known to impose particular structural motifs. Here the ability of a β/γ-dipeptide to replicate the backbone length of …

Advances In Raman Hyperspectral Compressive Detection Instrumentation For Fast Label Free Classification, Quantitation And Imaging, Bharat R. Makani

Open Access Dissertations

Multiple prototypes of hyperspectral compressive detection (CD) Raman spectrometers have previously been constructed in the Ben-Amotz lab and have proven to be useful for fast, label-free chemical identification, quantitation and imaging. The CD spectrometer consists of a volume holographic grating (VHG) that linearly disperses the Raman photons into its component wavelengths and all wavelengths are focused onto a digital micromirror devise (DMD). The DMD is an optical modulator that consists of an array of programmable 10μm mirrors that can reflect photons in either +12° or -12° to the incoming light. The DMD is tilted such that the +12° photons go …

Single-Conformation Spectroscopy Of Hydrogen Bonding Networks: Solvation, Synthetic Foldamers, And Neurodegenerative Diseases, Patrick S. Walsh

Open Access Dissertations

The hydrogen bond is one of the most important interactions in natural processes ranging from protein folding to chemical reactions. Two complementary methodologies are applied to understanding this important interaction: top-down and bottom-up. Top-down methods use large molecules, such as proteins, revealing secondary structure information. Bottom-up experiments are performed on small molecules, utilizing high-resolution spectroscopy to reveal underlying quantum mechanical effects. The complexity gap is formed between these two experimental regimes; between large and small molecules; between bulk and individual solvent molecules; between classical mechanics calculations and quantum chemical calculations. This dissertation will focus on the application of gas phase, …

Energy Transfer And Localization In Molecular Crystals, Mitchell A. Wood

Open Access Dissertations

With the aim of developing new technologies for the detection and defeat of energetic materials, this collection of work was focused on using simulations to characterize materials at extremes of temperature, pressure and radiation. Each branch of the work here is collected by which material response is potentially used as the detectable signal.

Where the chemical response is of interest, this work will explore the possibility of non-statistical chemical reactions in condensed-phase energetic materials via reactive molecular dynamics (MD) simulations. We characterize the response of three unique high energy density molecular crystals to different means of energy input: electric fields …

Mass Spectrometric Characterization Of Peptide Radical Ions And Implication For Radical Chemistry, Lei Tan

Open Access Dissertations

Gas-phase radical ion chemistry has attracted increasing research interest from the mass spectrometry (MS) society because it provides new capabilities in bio-analysis which often complements traditional MS methods developed from even-electron ions. Fundamental studies of biomolecule related radical species are essential to broadening the scope of radical chemistry and pushing the frontiers of its analytical applications. This dissertation mainly discusses the gas-phase chemistry of peptide sulfinyl radicals (-SO·), which has been rarely studied before. In order to establish an effective research approach, a method that can generate site-specific peptide sulfinyl radical ion has been developed. This method is based on …

Quantification Of Molecular Aggregation Equilibria Using Spectroscopic Measurements And Random Mixing Modeling, Blake M. Rankin

Open Access Dissertations

Molecular aggregation equilibria, such as the binding of ligands to a central solute molecule, are prevalent throughout biological processes and energy storage devices. However, both the sign and magnitude of hydrophobic and ionic interactions remains a subject of theoretical debate, and has yet to be experimentally determined. Here, Raman vibrational spectroscopy is combined with multivariate curve resolution (Raman-MCR) to experimentally quantify both the number of hydrophobic contacts between alcohol molecules in water and the affinity of ions for molecular hydrophobic interfaces. Furthermore, a generalized theoretical model is developed based on random statistics in which it is assumed that the concentration …

Supersonic Jet Spectroscopy Of Synthetic Foldamers, Multichromophores, And Their Water Containing Clusters, Evan Gardner Buchanan

Open Access Dissertations

A central theme specific to this dissertation concerns the conformation-specific spectroscopy of flexible molecules in an effort to bridge the complexity gap. Generally, molecules in the complexity gap have several flexible coordinates yet conformational isomerization still occurs along a simple reaction coordinate on the potential energy surface. Molecules in this regime benefit greatly from experiments probing the potential energy surfaces and provide a means to develop and test new theories in an effort to explain more complex system. These measurements are possible through the utilization of a supersonic jet expansion to collisionally cool molecules into their vibrational zero-point levels, collapsing …

Determination Of Disulfide Bond Connecting Patterns Via Tandem Mass Spectrometry (Msn) And Biomolecular Ion/Radical Reactions, Kirt Lenroy Durand

Open Access Dissertations

Disulfide bond formation is one of the most common post translational modifications to occur in proteins and naturally occurring peptides. Disulfide bond formation plays a critical role in stabilizing their three-dimensional structure; therefore, it is very important to pinpoint the correct disulfide bond connecting pattern in order to fully understand the biological functions of these proteins and peptides. To fully characterize an analyte containing disulfide bonds, the sequence must first be known followed by the disulfide bond connecting pattern. This presents an analytical challenge as there are very few methodologies that can produce those essential pieces of information. The gold …

Excited States Of Chromophores And Vibronic Interactions, Benjamin T. Nebgen

Open Access Dissertations

The main focus of my Ph.D. work has been on building a vibronic coupling model for multichromophores and extending that model to more general systems. This Dissertation serves as both a summary of this work as well as a manual for the two vibronic coupling programs I have written. It is my hope that the instructions written here are complete enough for any who would like to replicate my work on vibronic coupling on other systems. ^ Additionally, I have also worked on a few purely computational projects not directly related to the vibronic coupling work. The status of these …

Fundamental Studies On Copper Zeolites For Catalytic No X Abatement, Anuj Arun Verma

Open Access Dissertations

Stringent regulations in mobile NOx emissions have resulted in the development of Standard Selective Catalytic Reduction (SCR) as the dominant NOx abatement technology in lean burn diesel engines. Standard SCR is a reaction of nitric oxide (NO) with ammonia (NH₃), in the presence of oxygen (O ₂) to form nitrogen (N₂) and water (H₂O). Copper containing zeolites show commercially viable SCR performance. Cu-SSZ-13 (CHA framework), a member of this family, is a preferred catalyst for SCR applications because it shows exceptional hydrothermal stability in addition to commercially viable SCR performance. Our work focuses …

Reactivity Studies Of Tridhydropyridine Radical Cautions By Using Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry And Advancement Of Mass Spectrometric Analysis Of Asphaltenes And Degradation Products, Mohammad Sabir Aqueel

Open Access Dissertations

Aromatic organic molecules which have unpaired electrons play an important role in a variety of applications in the fields of organic synthesis, organic magnets, and biological activity of organic compounds. Several studies have been published on σ- type carbon-centered mono- and biradicals. Reactive intermediates with three formally unpaired electrons are known as triradicals. They can be defined as species with three electrons distributed in three degenerate or nearly degenerate orbitals, based on Salem's definition of biradicals from the electronic structure point of view. Very little is known about the reactivity of carbon-centered σ,σ,σ- triradicals due to the complexity of studying …

Construction And Demonstration Of A Tandem Mass Spectrometer Based Instrument For Cold Ion Spectroscopy, James Gerhardt Redwine

Open Access Dissertations

A new instrument incorporating ion trap based tandem mass spectrometry and cold ion UV and UV-IR double resonance spectroscopy has been developed at Purdue University for the study of gas phase, biologically relevant ions. The instrument incorporates multiple quadrupole linear ion trap mass analyzers to prepare and isolate the precursor ions as well as to analyze the resultant photofragments. A 22-pole ion trap cooled to 5 K via a closed cycle helium cryostat is used to cool the ions for spectroscopic interrogation. Results show the vibrational and rotational temperature of a wide assortment of ions to be 12±2 K.

The …

Gas-Phase Covalent And Non-Covalent Ion/Ion Chemistry Of Biological Macromolecules, John Robert Stutzman

Open Access Dissertations

Gas-phase ion/ion chemistry involves the interaction of oppositely charged ions inside of the mass spectrometer. During this gas-phase chemistry, particle transfer (i.e., proton and electron) or synthesis can occur at rapid reaction rates. Particle transfer represents a mature area of ion/ion chemistry, while selective covalent modification represents a fairly new area of gas-phase chemistry. Gas-phase covalent chemistry is based on traditional solution phase organic chemistry.

The work demonstrated in this dissertation greatly involves gas-phase covalent and non-covalent Schiff base chemistry on peptide and protein ions. The reagent dianion, 4-formyl 1,3-benzene disulfonic acid, has been used to covalently modify unprotonated primary …

Spectroscopic Characterization Of The Water-Oxidation Intermediates In The Ru-Based Catalysts For Artificial Photosynthesis, Dooshaye Moonshiram

Open Access Dissertations

Utilization of sunlight requires solar capture, light-to-energy conversion and storage. One effective way to store energy is to convert it into chemical energy by fuel-forming reactions, such as water splitting into hydrogen and oxygen. Ruthenium complexes are among few molecular-defined catalysts capable of water splitting. Insight into the mechanism of their action will help to design future robust and economically feasible catalysts for light-to-energy conversion. Mechanistic insights about the design of such catalysts can be acquired through spectroscopic analysis of short-lived intermediates of catalytic water oxidation. Development of time-resolved approaches through stopped flow UV-Vis Spectroscopy to follow the catalysis of …