Browsing by Subject "spectroscopy"

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3D Orientation of Alpha Helix in Muscle Myosin Regulatory Light Chain Using Bifunctional Electron Paramagnetic Resonance
(2021-06) Savich, Yahor
Muscle contraction is a coordinated work of nanometer-sized force generators, myosin molecules. These molecules are out of equilibrium: they use the energy stored in the form of ATP to move collectively along the track protein actin. The myosin molecules transfer their work via lever arms that connect force generators to their cargo. Orientation of these lever arms has been studied thoroughly since 1) their structural dynamics is fundamental for understanding the muscle contraction and 2) their particular orientations are associated with disease states of cardiac and skeletal muscle. Electron microscopy, fluorescence polarization, and X-ray diffraction have provided insight into the structure of muscle, but there is still no high-resolution data of the vertebrate lever arm orientation available at ambient (not vitriﬁed or crystallized) conditions. The present work establishes a method of measuring the orientation of the alpha helices in three dimensions using electron paramagnetic resonance (EPR). Chapter 3 introduces the use of EPR with bifunctional spin labels attached to different helices of the myosin regulatory light chain (RLC) protein with and without ATP. Demembranated skeletal muscle fibers were aligned with the slowly-varying magnetic field; RLC was chemically substituted by labeled RLC; axial orientational dynamics of the probe with respect to the muscle axis was determined. Chapter 4 utilizes 1) directional statistics that replaces the previous use of a Gaussian distribution and provides new insights into the degree of disorder and 2) a new bifunctional probe that adds an azimuthal dimension to the orientational data. Together, these techniques allow determination of the tilt and roll angles of the alpha helix without relying on the myosin structure.
Applied and extended modeling of optical interference effects towards sum frequency generation in multilayer thin films
(2021-10) Dramstad, Thorn
Sum frequency generation is a powerful technique to elucidate the molecular order and orientation of interfacial molecules where a bulk media typically prevents characterization. Additionally, optical interference effects further complicate analysis of the sum frequency response as constructive and destructive interference alter the intensity of the measured signal. Quantitative assignment of the interfacial molecules requires an accounting of the optical properties of the films to solve the present interference. Performance of this analysis requires a modeling routine. Current routines struggle with performance issues including slow functionality and a lack of user friendliness. Within this work, construction of a novel fitting routine is documented. The routine uses transfer matrix formalism to describe the optical propagation of light throughout the relevant thin film systems. It is applied to resolve interfacial questions for prototypical electronic materials. In the first chapter, the modeling is used to determine the packing of interfacial molecules as the thickness of the vibrationally active material is varied. In the second, I studied a system with a temperature-dependent packing structure. Following, the model is extended to explore the refractive indices: both their value and treatment. In Chapter 4, I offer a novel perspective by leveraging the optical inferences in a sum frequency generation experiment to solve the refractive indices, as the descriptive transfer matrix formalism is highly dependent on the complex terms. Finally, the description of the material boundary is explored, ranging from distinct to continuous, and the effects on the sum frequency signal are demonstrated in Chapter 5.
Electronic Transport in Semiconductor Nanocrystal Thin Films
(2018-06) Benton, Brian
Semiconductor nanocrystal (NC) thin films have emerged as intriguing materials for low cost synthesis of electronic devices with size-tunable optical and electronic properties that enable unique control over operating characteristics. However, in order to fully realize the potential of these materials so that they can be effectively integrated into useful devices, greater understanding of the electronic transport properties is needed. In particular, the relationship between film morphology, surface chemistry, and disorder leads to unique challenges in engineering the performance of NC-based devices. The standard measurement techniques and modeling schemes developed for bulk semiconductors are not necessarily well suited for these challenges, so a deeper understanding of how they can be applied to semiconductor NC films and how to properly interpret the results is needed. In this thesis, the electronic conduction in two semiconductor NC material systems was explored. First, ZnO was used as a wide bandgap material that was known to have high native doping levels and electronic conduction that can approach metallic behavior. Atomic layer deposition (ALD) Al2O3 was used to passivate thin films of porous ZnO NCs, which have electronic properties that are extremely sensitive to surface oxidation reactions with ambient water vapor. This property was utilized to systematically control the conductivity of ZnO films by photochemically desorbing surface hydroxyl groups in vacuum and performing subsequent electrical measurements in situ. With this technique, we observed conductance increases of up to 105 and associated changes in transport mechanism between Mott and Efros-Shklovskii variable range hopping regimes. Through this analysis, we were able to determine the role of defect states and NC surface depletion in determining the coupling between NCs. Second, Ge NCs were studied as a narrow bandgap material with large quantum confinement effects leading to bandgap increases of up to 50%. Thermal admittance spectroscopy (TAS) and field-effect transistor (FET) measurements were used together to study charge injection in these films. We observed a change from electron conduction to hole conduction in Ge NC FETs after infilling with ALD Al2O3. The dominant barrier for transport in these FETs was determined to be minority carrier injection to the channel due to NC charging. Contact material was not observed to have any effect on the FET polarity, which, along with large hysteresis observed in I-V and C-V measurements, indicates that the transport properties are largely dominated by trap states.
Investigations into the Dynamics and Reactivity of Excess Charges in Aliphatic Ionic Liquids
(2020-09) Knudtzon, Meghan
Ionic liquids (ILs) are a unique class of materials that have gained popularity for their potential use in a wide variety of energy applications. In these applications, ILs are subjected to highly ionizing radiation and electrochemical stress, which can produce excess charges resulting in degradation and device failure. Understanding the relationship between the molecular structure of ILs and the sub-nanosecond dynamics of these excess charges is crucial to developing robust liquids tailored to specific applications. The first section of this dissertation characterizes the transient absorption and excess charge dynamics in 1-butyl-1-methyl-pyrrolidinium dicyanamide ([Pyr1,4][DCA]) following excitation at 4.66 eV. The results were compared to previous work from our group on an analogous system to determine the influence of the anion on the initial state of the excess electron and subsequent solvation dynamics. Next, the impact of cation structure is examined in the [Pyr1,x][DCA] series by in- creasing the length of the alkyl tail. The length was found to influence the absorption energy of the free electron, as well as the relaxation dynamics and competition between relaxation pathways. The third section addresses the hypothesis of the [NTf2 ] anion serving as an electron scavenger in the [Pyr1,4][DCA] liquid. The addition of the [NTf2 ] was found to have little impact on the excitation of the electron and subsequent relaxation dynamics. It was concluded that the excitation energy was selectively exciting electrons in [DCA]-rich domains, resulting in dynamics analogous to neat [Pyr1,4][DCA]. The final section of this dissertation explores the impact of excitation process on the solvation dynamics of excess electrons by comparing results from pulse radiolysis in [Pyr1,4][DCA] to the photolysis in the first section. The work was performed at Brookhaven National Lab in partial fulfillment of the research proposal funded by the U.S. Department of Energy’s Office of Science Graduate Student Research (SCGSR) Program. The pulse radiolysis technique was complimentary to the photolysis work performed at the University of Minnesota and allowed the relaxation dynamics to be examined in a larger time window.
Leveraging Polarized Metal-Metal Bonds for Catalytic Hydrodefluorination via Thermal and Photolytic Pathways
(2020-12) Moore, James
Organofluorines are pervasive in our everyday lives and found in many commodities and chemicals, including pharmaceuticals, agrochemicals, and lubricants. The utility of organofluorines is due largely to the unique properties imparted from fluorination, with the most notable being the enhanced stability and greatly increased lifetime. However, the increased stability and widespread production of organofluorines has led to widespread environmental contamination, which is especially problematic due to the toxicity of perfluorinated organic molecules. Hence, it is crucial to develop catalysts that are capable of efficiently cleaving the strong C–F bonds in these persistent chemicals. One emerging strategy that has been used to cleave strong bonds is the utilization of bimetallic complexes featuring polarized metal–metal bonds. This dissertation investigates the use of bimetallic complexes comprised of late transition metals (Fe and Rh) supported by Lewis acids, including Ti, Al, Ga, and In, for the hydrodefluorination of fluorinated organics. These complexes were characterized using a suite of spectroscopic, electrochemical, and computational methods to probe the electronic effect that the Lewis acid has on the late transition metals. Overall, it was found that the Rh complexes supported by the group 13 metalloligands were highly active for the cleavage of unactivated aryl C−F bonds using mild heat. Moreover, these same complexes were also found to be highly reducing photoredox catalysts that were capable of reducing and subsequently cleaving unactivated aryl and benzylic C–F bonds using visible light. Overall, this work demonstrates the utility of polarized metal–metal bonds in homogenous defluorination catalysis, welcoming a new paradigm in the activation of the strongest bonds.
Phase Resolved Infrared Imaging and Spectroscopy of Phonon Modes in A Wide-Bandgap Epitaxial Semiconductor
(2023) MacDonald, Shane
In this thesis, the novel design of a Phase-Resolved Infrared Spectroscopy Microscope (PRISM) was described and constructed, then demonstrated to have an imaging spatial resolution of ~ 7.6 μm. The PRISM was placed within an asymmetric Michelson-based interferometer which allowed for pseudoheterodyne detection as well as Fourier Transform Infrared Spectroscopy (FTIR) of infrared reflection on a sample. Using PRISM, experimental data was collected consisting of reflectance images and spectroscopy of IR-active optical phonon modes in the tetragonal and orthorhombic phases of an epitaxial strontium stannate (SSO) sample at different incident light polarizations. The analysis and fitting process to determine the permittivity of the substrate and SSO thin film was then described and implemented. The analysis yielded the permittivity of the SSO film in the tetragonal and orthorhombic phases, providing new insight into the mobility-limiting phonon modes of epitaxial SSO.
Plasmon Hybridization In Self-Assembled 3D Graphene-Based Metamaterials
(2020-04) Agarwal, Kriti
Three-dimensional (3D) photonic geometries are attractive for developing novel coupled optical modes that cannot exist in the two-dimensional (2D) nano and microfabrication world. In this thesis, the various optical properties that can be induced as a result of 3D architecture are designed, fabricated, and characterized. Even for the well-established resonance in split-ring resonator-based metamaterials, the addition of the multiple planes of symmetric coupling or decoupling induce isotropic and anisotropic resonances for applications such as ultra-sensitive molecular analysis with two-fold advantage of frequency and amplitude monitoring for small concentrations and low on-chip power inclinometers with nanodegree sensitivity, respectively. The limited spatial coverage of the plasmon-enhanced near-field in 2D graphene ribbons presents a major hurdle in practical applications. The ability to transform 2D materials into 3D structures while preserving their unique inherent properties offers enticing opportunities for the development of diverse applications for next-generation micro/nanodevices. Diverse self-assembled 3D graphene architectures are explored here that induce hybridized plasmon modes by simultaneous in-plane and out-of-plane coupling to overcome the limited coverage in 2D ribbons. While 2D graphene can only demonstrate in-plane bi-directional coupling through the edges, 3D architectures benefit from fully symmetric 360° coupling at the apex of pyramidal graphene, orthogonal four-directional coupling in cubic graphene, and uniform cross-sectional radial coupling in tubular graphene. The 3D coupled vertices, edges, surfaces, and volumes induce corresponding enhancement modes that are highly dependent on their shape and dimensions. While most of this work strives to achieve multiple coupled planes of symmetry, the same ideas are also applied to achieve multiple 3D graphene geometries that break mirror symmetry across multiple planes. The asymmetric graphene induces giant optical activity (chirality) that has remained previously unrealized due to the 2D nature of graphene. The chirality induced within the 3D graphene chiral helixes is also a strong function of the geometrical parameters that are analyzed using a machine-learning-based multivariate regression approach to determine the 3D geometry with the strongest chirality. The hybrid modes introduced through the 3D couplings amplify the limited plasmon response in 2D ribbons to deliver non-diffusion-limited sensors, high-efficiency fuel cells, and extreme propagation length optical interconnects.
Spectral Deconvolution and Quantification of Natural Organic Material and Fluorescent Tracer Dyes
(Proceedings of the Tenth Multidisciplinary Conference on Sinkholes and the Engineering and Environmental Impacts of Karst. © 2005 American Society of Civil Engineers. Published online: April 26, 2012, 2005-09-28) Alexander, Scott C
Fluorescent dyes have become an integral part of the study and management of ground water in karst environments. Researchers have striven to reduce detection limits and analyze multiple dyes in a single sample while minimizing dye concentrations for environmental, aesthetic and health reasons. The unambiguous separation from background, identification and quantification of fluorescent tracer dyes has increasingly taken on legal implications. Synchronous fluorescence spectroscopy and curve fitting software represent a major advances in the quantitative analysis of low levels of tracer dyes against naturally occurring background fluorescence. Determination of levels of detection (LOD) and levels of quantification (LOQ) are an important part of dye trace design and implementation. Factors that impact LOD and LOQ include levels of natural fluorescent compounds, absolute fluorescence of the specific dyes, the presence of multiple dyes with overlapping peaks and instrumental noise. Characterization of the spectral shapes and concentration dependences of the natural fluorescence background and applied tracer dyes are important to the determination of a positive dye trace result. Rather than representing noise, the natural fluorophores contain information about the flow environment. Spectral deconvolution with curve fitting software is an important tool in the karst researcher’s toolbox.
Spectroscopic and Structural Analysis of Oxygen-Activating Nonheme Diiron Enzymes and Related Synthetic Models
(2017-05) Jasniewski, Andrew
The general mechanism of O2 activation by nonheme diiron enzymes begins when the diferrous iron cluster binds dioxygen. The diiron cluster is oxidized to a peroxo-diferric intermediate that in some cases reacts directly with substrates, and in others becomes further activated via the cleavage of the O–O bond, leading to the generation of a potent high-valent oxidant that is the active oxidant for the cycle. Peroxo-diferric intermediates are of high interest because they are crossroads between the use of peroxo-diferric or high-valent oxo intermediate as the active oxidant in diiron-cluster-mediated oxidase and oxygenase chemistry. Understanding this O2 activation process requires structural characterization of enzymatic peroxo-diferric species. Spectroscopic methods, like electronic absorbance, X-ray absorption (XAS), and resonance Raman (rR) spectroscopies are used to probe a rich landscape of oxygen-activated intermediates and obtain detailed structures of these species. Through systematic study, insight can be gained into the mechanisms of these biological systems and ultimately this insight can be used to understand how Nature has chosen to use peroxo-diferric intermediates for a variety of different functions. In Chapter 2, X-ray diffraction and XAS were used to characterize various form of the enzyme CmlA to understand how O2 is regulated in the presence and in the absence of its non-ribosomal peptide synthetase (NRPS) bound substrate. In Chapter 3, the intermediate species on the O2 activation pathway of the human enzyme deoxyhypusine hydroxylase (hDOHH), including the µ-1,2-peroxo species, were studied using XAS. The structural analysis of the active sites of the various hDOHH species provided insight into the reaction mechanism for the system. In Chapter 4, XAS and rR studies on the unusual peroxo-diferric species of the N-oxygenase CmlI were carried out. The spectroscopic analysis of the peroxo intermediate describes a new peroxo binding geometry for diiron enzymes, a µ-1,1-peroxo species. In Chapter 5, detailed XAS characterization of various synthetic peroxo-diferric and oxoiron(IV) model complexes is described. Overall, this thesis demonstrates the power of structural characterization by complementary spectroscopic methods to support and generate enzymatic mechanistic hypotheses.
Structural Investigation of Electron-Beam Sensitive Zeolites and Metal-Organic-Frameworks Using Analytical Transmission Electron Microscopy
(2018-08) Kumar, Prashant
An interesting class of materials that has become ubiquitous in our daily lives is the family of zeolites, which are porous scaffolds made of silicon, oxygen and aluminum atoms. Zeolites act like a coffee filter paper with pores of molecular dimensions that can be tailored to separate molecules of different diameters by adjusting the sizes of the pore openings from 2 Å (1 Å = 0.0000000001 m) to 10 Å. For example, over 90% of commercially available detergents contain zeolites, which act as water softeners by selectively removing calcium and magnesium ions from water, while any product that can be traced back to a petrochemical refinery (like fuels, chemicals and pharmaceutics) contains molecules that have passed through selective zeolite pores numerous times. To date, 231 unique zeolite frameworks have been synthesized while computer simulations predict over 330,000 new structures. TEM imaging and electron diffraction has contributed in the crystal structure determination of many of the known 231 synthesized zeolite frameworks. However, the recent development of few-atom-thick zeolites (2-dimensional zeolite nanosheets) and new classes of porous materials based on metal-organic-frameworks (MOFs) pose new demands and create new opportunities for electron microscopy. The objective of this dissertation work is to determine the atomic arrangement in zeolite nanosheets and metal organic frameworks using transmission electron microscopy to develop a fundamental relationship between their crystal structure and performance as catalysts and membranes. Using electron diffraction, imaging, spectroscopy and digital image processing, TEM data acquisition and analysis routines have been developed to mitigate electron beam sensitivity of these materials. Implementation of the developed routines enabled crystal structure, growth and defect analysis down to the atomic scale, leading to novel findings and implications discussed in detail here.
Structural- and Spectroscopic-Reactivity Relationships of Nonheme Oxoiron(IV) Complexes
(2019-05) Rasheed, Waqas
Non-heme oxoiron(IV) motifs have been identified as key intermediates that activate strong C—H bonds. Unlike the enzymatic intermediates however, most oxoiron(IV) complexes in synthetic chemistry have a triplet ground spin state and thus differ in their functional and electronic properties from the S = 2 units characterized in the enzymes. One striking exception is the complex [FeIV(O)(TQA)(L)]2+, where TQA = tris(2-quinolylmethyl)amine, which has Mössbauer parameters that closely resemble those of TauD-J, an enzymatic intermediate that has been relatively well-characterized. This oxoiron(IV) complex contains quinoline donors, and its thermal instability precludes its structural characterization (half-life = 15 minutes at 233 K). In this dissertation, several oxoiron(IV) complexes supported by pentadentate and tetradentate ligands are characterized, and examined for their reactivity and spectroscopic features. Crystallographic characterization of a few of these molecules is also reported. The structurally characterized oxoiron(IV) complexes along with some previously reported oxoiron(IV) complexes are used to set up structure-reactivity and spectroscopic-reactivity relationships, and show linear correlations with increasing isomer shifts, λmax values as well as metal-ligand distances. In addition, this thesis also uses 1H-NMR spectroscopy as an effective tool to identify solution-state structure as well the spin state of oxoiron(IV) complexes. We also characterize the first example of a spin crossover oxoiron(IV) complex, examples of which are only seen in iron(II) and iron(III) complexes.

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