Deeper understanding and technological progress in materials physics demand exploration of soft and hard matter at their relevant length scales. This research focuses on the nanometer length scale investigation of structural changes required for membrane fusion in virus nanoparticles and nano-spectroscopic investigation of layered material surfaces implementing scattering type scanning near-field optical microscopy (s-SNOM). Spectroscopy and imaging experiments were deployed to investigate the chemical and structural modifications of the viral protein and lipid bilayer under various environmental pH variations. It has been shown that breakage of viral membrane could occur even without the presence of a targeting membrane, if the environment pH is lowered. This is in contrary to the current viral fusion model, which requires virus binding to a host cell membrane for forming the fusion pore to release the viral genome. The fusion inhibitor compound 136 can effectively prevent the membrane breakage induced by low pH. The chemical surface stability and degradation of black phosphorus (BP) under ambient conditions have been studied using s-SNOM. We found that the degraded area and volume on the surface of black phosphorus increase with time slowly at the start of degradation and enlarge rapidly (roughly exponentially) afterward and reach saturation growth following S-shaped growth curve (sigmoid growth curve). The theoretical model presented suggests that the degraded sites in the adjacent surrounding causes the experimentally observed exponential growth of degraded area at the initial stage. By studying the BP surfaces coated by Al2O3, boron nitride (BN) and hybrid BN/Al2O3 layers through the period up to 6 months, it has been concluded that ~5 nm thin hybrid layer of BN/Al2O3 helps the surface passivation of BP flakes of thickness ~30 nm. This is supported by the electrical characterization results of BP field effect transistor coated with a BN/Al2O3 layer. We have performed infrared nano-spectroscopy on muscovite mica exfoliated on silicon and silicon dioxide substrates. We show that the near-field profile in s-SNOM can penetrate down to several hundreds of nanometers and enable spectroscopy of buried structures. We found spectral broadening of mica as its thickness increases revealing clearly the effect of size on the absorption response.

L’insuffisance rénale chronique (IRC) et l’une des pires maladies chroniques dans les pays développés. Les grades de l’IRC sont principalement basés sur la mesure ou l’estimation du taux de filtration rénale (GFR). Cependant, cette méthode est peu sensible sur les premiers stades de la pathologie et n’apporte donc pas de valeur diagnostique. La détection de la pathologie à des stades précoces et son traitement peuvent éviter ou limiter les effets délétères de la chronicité. Cette thèse se penche sur le développement de la microscopie IRTF en tant qu’outil diagnostic pour l’identification par histopathologie à l’échelle du glomérule dans un modèle d’IRC. Nous avons développé la technique de reconstruction 3D pour l’imagerie IRTF des modifications biochimiques à l’échelle du glomérule pour déterminer des marqueurs de l’IRC. La déconvolution spectrale et le clustering sont appliqués après analyses IRTF pour distinguer les modèles sains et pathologiques. Ensuite, la microvasculature glomérulaire est révélée par agent de contraste pour en déterminer les anomalies morphologiques. Grâce aux résultats obtenus en 3D et l’utilisation de méthodes statistiques avancées, la microscopie IRTF est utilisée comme une technique fonctionnelle pour déterminer les modifications morphologiques et moléculaires apparaissant au cours du développement de l’IRC. / CKD (Chronic Kidney Disease) is one of the worst public diseases in developing countries. The stages of CKD are mainly based on measured or estimated GFR (Glomerular Filtration Rate). However, this method is not sensitive enough on early stages of the pathology and thus do not offer accurate diagnostic value. Early detection and treatment can often limit or avoid the chronicity effects of the disease. This thesis focuses on the development of FTIR microscopy as a diagnostic tool for the identification by histopathology at glomerulus level of the kidney in CKD model. We developed a technique of 3D reconstruction for the FTIR imaging of biochemical components changes in glomeruli for identifying the pathological marker of CKD. The curve-fitting and spectral clustering are applied on the FTIR microscopy analysis to distinguish between healthy and pathological glomeruli of a kidney. Then, the glomerular microvasculatureis highlighted to reveal the morphological abnormalities by perfusing contrast agents into blood vessels. With advanced 3D statistical methods and 3D image visualization by microscopy, FTIR spectro-imaging can be used as a functional technique to determine the morphological and molecular changes occurring along CKD development.

Overhead conductors used in the transmission of power in grids around the world are generally subjected to ageing, which is the time-based change of their properties. Important properties such as corona discharge, audible noise, hydrophobicity and corrosion are usually considered and investigated. On some conductors such as the aluminium conductor steel reinforced (ACSR), a reduction in audible noise over exposure time to the service environment has been noted to occur. However, the converse has been observed for the gap-type thermal resistant aluminium conductor steel reinforced (GTACSR or “Matthew” conductor), although this conductor is preferred due to its high ampacity. The relationship between conductor hydrophobicity, audible noise, surface contamination and roughness, wettability and corrosion were investigated using All Aluminium Alloy Conductor (AAAC), Aluminium Conductor Composite Core (ACCC) and GTACSR samples. Findings from Fourier Transform Infrared Spectroscopy (FTIR), X-ray Photoelectric Spectroscopy (XPS) and contact angle measurements revealed that carbon, hydrocarbon and silicone contamination was responsible for the hydrophobic nature of the surface. Furthermore, electrochemical investigations and electron microscopy showed that pitting or/and crevice corrosion were the predominant corrosion mechanisms on these conductors. Exposure to simulated industrial and marine environments further confirmed this finding and also showed that general corrosion also occurs on relatively uncontaminated conductors, thereby changing their surface roughness, as seen from the White Light Interferometry results. Corrosion was observed to be accelerated by the presence of surface contaminants such as oils and carbon, as these facilitated water (droplet) retention by reducing the conductor’s surface energy. Reduction/elimination of surface contamination/hydrophobicity were the desired solutions to the problem, and this was achieved by grit blasting. Partial/complete oxidation of the silicones resulted in the reduction/elimination of sample hydrophobicity – this was seen from more contact angles measurements and XPS data. Grit blasting also restored conductor cleanliness and roughened the surface sufficiently to produce surface run-off.

Absorption of octadecanethiol and p-nitrobenzenethiol onto gold surfaces from ethanol solutions has been studied by means of contact angle, optical ellipsometry, angle-resolved XPS (ARXPS), and with grazing angle total reflection FTIR. Growth of the monolayers from dilute solutions has been monitored and Langmuir isotherm adsorption curves were fitted to experimental data. A saturated film is formed within approximately 5h after immersion in solutions of concentrations ranging from 0.0005mM to 0.01mM. We found, that the final density of monolayer depends on the concentration of the solution.

This master’s thesis deals with the plasmon resonance of the nanostructures of several selected tungsten oxides using Fourier transform infrared spectroscopy (FTIR spectroscopy). The physical principles of the plasmonics, the characteristics of the materials used, as well as the principle of operating and measuring on the FTIR spectrometer, are described in the first part of this thesis. The second part is focused on the preparation of samples and performing measurements on the FTIR spectrometer. This part ends by representing the final spectra and the results obtained.

The functional and pathogenic roles of biomolecules are often coupled to the self-association of their basic units into oligomers and aggregates whose structural details are difficult to distinguish because of their insoluble and heterogenous nature. This work focuses on DNA G-quadruplex motifs and amyloid peptides whose oligomers and aggregates are associated with numerous biological roles and human diseases. Infrared (IR) spectroscopy is a powerful tool which probes vibrational transitions whose signatures report on their arrangement within molecules. Advances in two-dimensional infrared (2D IR) spectroscopy have allowed structural characterization in increasingly complex biomolecules that are not amenable to traditional high-resolution techniques. However, careful consideration of the physical phenomena that lead to IR spectra are necessary to make accurate assignments. In the first portion of this work, using FTIR and 2D IR, we determine spectral markers that can differentiate size, metal ion coordination, and topology in DNA G-quadruplex motifs. IR studies aided by isotope labeling define the physical origin of these markers and allow for the construction of a structural landscape in parallel DNA G-quadruplex motifs. It is also shown that 2D IR and isotope editing probes site-specific structural changes in G-quadruplex motifs that can differentiate ion identity and location based on spectral shifts. In the latter portion of this work, we use a combination of spectroscopy and imaging techniques to show that a peptide derived from the human pro-apoptotic protein BAX forms amyloid aggregates whose structure is dependent on the presence of model membranes. Combined, the work in this thesis allows for the formulation of multiple hypotheses based on IR structural assignments regarding disease states and functional mechanisms of these systems.

Amyloid aggregation involves the spontaneous formation of fibers from misfolded proteins. This process requires low energy input, results in robust fibers, and is thus of interest from a materials manufacturing perspective. The effect of glutamine content and hydrophobicity of template peptides on amyloid aggregation of a template-peptide system involving myoglobin was studied at near-physiological conditions by Fourier transform infrared spectroscopy, atomic force microscopy, field emission scanning electron microscopy, and nanoindentation. Hydrophobic interactions were found to be important for controlled hierarchical fiber growth via a cooperative mechanism, with the largest effect in myoglobin mixtures. Hydrophobic packing increased for most systems as aggregation progressed. The largest changes in structure occurred upon drying. When myoglobin was present with the highest glutamine-containing template (P7), the high glutamine peptide was not effective as a template, since it appeared to prefer self-catalysis. A low level of glutamine in some unordered templates was insufficient for amyloid development. However, templating was more important in glutamine-free templates mixed with myoglobin, which formed fibers with a surprisingly high elastic modulus. This may have been due to template patterning. Nanoindentation results confirmed that glutamine blocks were not necessary for strong intermolecular interactions and cooperative fibril formation. / Master of Science

Thesis advisor: Matthias M. Waegele / Studying the adsorption and reaction kinetics of surface-bound chemical species, on different metal catalysts or electrodes, is of paramount importance in the development of inhomogeneous catalytic methodology. Our study of the oxidation of CO on platinum was accomplished by designing a thin layer flow cell in an external reflection configuration. A charge-injection circuit was successfully implemented which decreased the time required to charge the double layer in the electrochemical cell. We were able to obtain a signal via Stark shift spectrum, of the adsorbed CO, using the thin layer cell configuration. Additionally, electrochemical impedance spectroscopy was used as a diagnostic tool to assess the effect of electrode geometry, on the voltage response, in the thin layer cell. The coupling of visible light-driven photoexciation with transition metal catalytic plat- forms is emerging as a synthetic strategy to achieve unique reactivity that has previously been inaccessible. One such example is the iridium/nickel-dipyridyl system discovered recently. Characterizing the interactions between the iridium and nickel catalysts, under reaction conditions, is important to develop a better understanding of the system. In order to apply infrared spectroscopic measurement techniques, in-situ, we made modifications to the synthetic scheme by changing the solvent and by utilizing different iridium catalysts for the synthesis of the desired methyl 4-(benzoyloxy)benzoate product. Using our trans- mission infrared setup we effectively demonstrated in-situ product detection of the aryl- ester coupled product. Additionally, after constructing a transient infrared pump-probe setup, we collected preliminary results of the triplet state lifetime of the iridium dye. The surface morphology of copper has been shown to affect the electrochemical reduction of CO2. Using surface-enhanced Raman spectroscopies, the reversible formation of nanoscale metal clusters on a copper electrode was revealed at sufficiently cathodic potentials where we observed the appearance of a new band at 2080 cm-1 corresponding to C≡O adsorbed to undercoordinated copper defect sites. The formation of new undercoordinated sites additionally resulted in the surface enhancement of the Raman scattering which amplified the intensity of the other spectral bands. / Thesis (MS) — Boston College, 2019. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Indiana University-Purdue University Indianapolis (IUPUI)

Blood is one of the most common biological fluids encountered at crime scenes and is therefore constantly being tested for in the laboratory. Confirming the presence of blood can illuminate essential elements of a case as well as allow for identification via downstream DNA analysis. This significant investigative value is why it is crucial to use robust forensic testing techniques for blood detection. In the forensic laboratory, blood is identified using serological techniques. A presumptive test, such as a colorimetric test, is performed first. A confirmatory test, such as an immunochromatographic assay, is often performed following a presumptive positive result. While both types of tests have numerous advantages, they have several limitations as well. These limitations have served as the basis for exploring alternative techniques for forensic blood detection, such as FTIR. FTIR spectroscopy is a qualitative, non-destructive, confirmatory analytical technique. This technique uses infrared light to characterize organic compounds based on molecular structure. There are also several different FTIR techniques, such as ATR and DRIFTS. ATR-FTIR analysis has been widely researched for the detection of blood and other biological fluids, across several applications. ATR-FTIR may be preferable to serological blood detection because it can be quicker than combined serological blood testing, it requires minimal sample preparation, it does not damage DNA downstream, and it can detect multiple biological fluids at once. Despite all the advantages that ATR-FTIR analysis has over traditional forensic blood techniques, it has not yet been implemented in casework. This may be due to skepticism in using subjective and complex spectroscopic data that results from ATR-FTIR analysis of body fluids. The initial objective of this research was to develop an optimized protocol using ATR-FTIR and chemometric analysis to identify blood on cotton round substrates. Using these techniques together would allow for a rapid, nondestructive, confirmatory approach, that would be more objective than serological testing or FTIR analysis alone. However, due to complications throughout the research process, this objective was altered. The revised objective was to develop an optimized protocol using DRIFTS and chemometric analysis to identify blood on cotton round substrates. An optimized DRIFTS protocol for forensic blood identification was successfully developed. Blood samples from multiple donors were tested using this protocol, and all samples showed similar data. Human biological samples other than blood as well as non-human samples were also tested. These samples showed dissimilar data from the donors’ blood sample data. Chemometric analysis was then performed using AnalyzeIQ Lab software. After testing 93 pair-wise combinations of pre-processing methods and algorithms, a model was developed. Unfortunately, this model was not completely optimized. It had a 9.09% error rate, resulting from the misclassification of one sample. Future research is needed before implementation into casework. Alternative cotton substrates and data collection software should be considered. Additional time should be spent using AnalyzeIQ Lab software, to develop a model with a 0% error rate. If this cannot be achieved, an alternative chemometric analysis software should be considered.