This thesis is concerned with coherent effects in high resolution mid-infrared gas phase spectroscopy using quantum cascade lasers (QCLs). An introductory chapter explains the importance of QCLs as radiation sources in the mid-infrared region of the spectrum and goes on to detail their development and structure. A discussion of coherent effects in spectroscopy follows, leading into the second chapter which discusses the theories relevant to the experimental sections of the thesis. In chapter 2 the theory underpinning direct and velocity selective, Doppler-free spectroscopy is discussed and a density matrix formalism is followed to derive the equations of motion that govern coherent excitation effects in two-level systems. In the final part of the chapter this treatment is extended to three-level systems. The equations derived in this chapter form the basis of quantitative interpretations of the phenomena observed in experimental data and presented in the remainder of the thesis. In chapter 3 the characterisation of a high power, narrow linewidth QCL is carried out. This laser is then used to perform direct and sub-Doppler resolution spectroscopy on NO, demonstrating non-linear absorption at high laser intensities and providing a measurement of the laser linewidth in the limit of slow frequency tuning. As the slow tuning rate increases, evidence of coherent transient effects is presented and density matrix theory used to model this behaviour. The data presented include the first observations of asymmetric Lamb dips and the onset of rapid passage oscillations from a Lamb dip. Pump-probe experiments on NO, utilising two cw QCLs are presented in chapter 4. The high level of velocity selection afforded by QCL excitation leads to coherent transient signals at far lower probe scan rates than previously reported. The effect of altering both the scan rate and the gas pressure and the importance of hyperfine structure are presented. A radio frequency noise source applied to one of the lasers is shown to broaden the laser linewidth, leading to rapid dephasing. A two-colour polarisation spectroscopy experiment is also presented which allows the measurement of both the absorption and the Doppler-free dispersion signals and the three-level density matrix formalism presented at the end of chapter 2 used to model the non-linear response of the system. The final chapter details the use of an acousto-optic modulator to create a pulse of mid-IR light using a cw QCL and the application of this to time resolved pump-probe spectroscopy. This capability suggests the prospect of achieving coherent population transfer by stimulated Raman adiabatic passage (STIRAP) using two such pulses. Simulations based on a simple three-level model and including Zeeman coherences are presented, which take the measured properties of the lasers used in this thesis as inputs to predict the potential population transfer achievable in NO as well as providing useful information about the angular momentum polarisation of the excited molecules. An experimental realisation of STIRAP would require the lasers to be stabilised, and so the final part of the chapter details experimental attempts to achieve stabilisation of an external cavity QCL, and suggests future avenues for improved implementation.

Cell penetrating peptides (CPPs) have drawn the attention of researchers due to their ability to internalize large cargos into cells including cancer cells. The mechanism(s) with which the peptides enter the cell, however, is/are not clear and full of controversy. The peptide conformations and their microenvironment in live cells had been unknown until the development of a technique developed in our lab. As a first demonstration of principle, penetratin, a 16-residue CPP derived from the Antennapedia homeodomain protein of Drosophila, was measured in single, living melanoma cells. Carbon-13 labeling of the Phe residue of penetratin was used to shift the intense aromatic ring-breathing vibrational mode from 1003 to 967 cm-1, thereby enabling the peptide to be traced in cells. Difference spectroscopy and principal components analysis (PCA) were used independently to resolve the Raman spectrum of the peptide from the background cellular Raman signals. / On the basis of the position of the amide I vibrational band in the Raman spectra, the secondary structure of the peptide was found to be mainly random coil and b-strand in the cytoplasm, and possibly assembling as b-sheets in the nucleus. Next, label-free transportan was studied with the same methodology. The peptide, besides predominantly a-helix, adopted a significant portion of b-sheet conformation in the cytoplasm and nucleolus, which is different from the peptide in aqueous solution. The peptide microenvironment was also probed through H-bonding reported by the tyrosine Fermi doublet. Transportan displayed a tendency to accumulate in the cytoplasm over time which was unlike penetratin, which concentrated in the nucleus. The relative concentration of CPPs in various locations of live melanoma cells was directly estimated from the Raman spectra using average Phe concentration in the cell as an internal standard. / The rapid entry and almost uniform cellular distribution of both peptides, as well as the lack of correlation between peptide and lipid Raman signatures, indicated that the mechanism of CPP internalization under the conditions of study was probably non-endocytotic. Last, transportan and penetratin were studied using polarized Raman spectroscopy for more detailed vibrational spectroscopic information of the two peptides in water and TFE solutions. The majority of the bands in the Raman spectra of the peptides were highly polarized, consistent with the high symmetry of aromatic ring side chain vibrational bands dispersed throughout the spectra. This work has provided new insights into the structure of CPPs in live cells and in solutions. / by Jing Ye. / Thesis (Ph.D.)--Florida Atlantic University, 2011. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2011. Mode of access: World Wide Web.

Foram estudados através de espectroscopia vibracional, Raman e infravermelho, uma série de derivados do íon pentacianocobaltato(II), de fórmula geral [Co(CN)5-L-Co(CN)5]n-, onde L é H2C=CH2, H3COOC-C=C-COOCH3, C2H5COO-C=C-COOC2H5, SO2, O--2, O-2 ou NO2. Além desses Complexos, o íon dímero [Co2(CN)10]6- também foi objeto de estudo. No caso dos íons [Co(CN)5-L-Co(CN)5]n- os espectros vibracionais na região de estiramento CN são interpretados com base numa simetria C4v dos grupos Co(CN)5 isolados. A natureza das ligações C=N e das, ligações do ligante L para esses compostos é discutida com base nos resultados obtidos. / The vibrational spectra (Raman and infrared) of a series of compounds of general formula [Co(CN)5-L-Co(CN)5]n-, derived from the pentacianocobaltate(II) ion, where L is H2C=CH2, H3CCOO-C=C-COOCH3, C2H5COO-C=C-COOC2H5, NO2, SO2, O--2 or O-2, were studied. The dimer ion [Co2(CN)10]6- has also been subject of study. In the case of the [Co(CN)5-L-Co(CN)5]n- ions the vibrational spectra in the region of CN stretching vibrations were interpreted based on the C4v symmetry of the isolated Co(CN)5 groups. Characteristic frequencies of the ligand L and skeletal vibrations of Co(CN)5 group are tentatively assigned. The nature of C=N bonding and the structure of ligand L for these compounds are discussed on the basis of the obtained spectral results.

by Ka-wai Wong. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1995. / Includes bibliographical references (leaves 106-109). / TABLE OF CONTENTS --- p.i / ABSTRACT --- p.v / LIST OF FIGURES --- p.vi / LIST OF TABLES --- p.xi / LIST OF ABBREVIATIONS --- p.x / Chapter Chapter 1 --- Research Background --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- The effect of solid acceptance angle --- p.2 / Chapter 1.3 --- Research goals --- p.4 / Chapter 1.3.1 --- Determination of the electron spectrometer transmission function --- p.4 / Chapter 1.3.2 --- Novel depth profiling technique by adjusting the solid acceptance angle --- p.6 / Chapter 1.3.3 --- Correction to conventional ARXPS --- p.8 / Chapter 1.4 --- Thesis Structure --- p.8 / Chapter Chapter 2 --- Fundamentals of X-ray Photoelectron Spectroscopy --- p.9 / Chapter 2.1 --- Introduction --- p.9 / Chapter 2.2 --- X-ray Photoelectron Spectroscopy (XPS) --- p.9 / Chapter 2.2.1 --- Basic principles --- p.9 / Chapter 2.2.2 --- Surface sensitivity --- p.11 / Chapter 2.2.3 --- A typical XPS spectrum --- p.13 / Chapter 2.3 --- Qualitative analysis --- p.16 / Chapter 2.3.1 --- Binding energy --- p.16 / Chapter 2.3.2 --- Chemical state information --- p.17 / Chapter 2.4 --- Quantitative analysis --- p.20 / Chapter 2.4.1 --- Factors affecting intensity --- p.20 / Chapter 2.4.2 --- Homogeneous materials --- p.22 / Chapter 2.4.3 --- Layer structure --- p.23 / Chapter Chapter 3 --- Instrumentation --- p.26 / Chapter 3.1 --- XPS spectrometer --- p.26 / Chapter 3.1.1 --- Magnetic immersion lens system --- p.26 / Chapter 3.1.2 --- Tunable iris --- p.29 / Chapter 3.1.3 --- Scan plates --- p.29 / Chapter 3.1.4 --- Input lens aperture --- p.32 / Chapter 3.2 --- Calibration of the iris --- p.32 / Chapter 3.3 --- Applications --- p.35 / Chapter 3.3.1 --- Two dimensional XPS imaging --- p.35 / Chapter 3.3.2 --- ARXPS --- p.37 / Chapter 3.4 --- Summary --- p.37 / Chapter Chapter 4 --- Determination of electron spectrometer transmission function --- p.38 / Chapter 4.1 --- Introduction --- p.38 / Chapter 4.2 --- Traditional method of determination --- p.39 / Chapter 4.3 --- Methodology of the novel approach --- p.40 / Chapter 4.4 --- Calculation Procedures and Results --- p.48 / Chapter 4.5 --- Results and Discussions --- p.50 / Chapter 4.6 --- Conclusions --- p.57 / Chapter Chapter 5 --- "Depth Profiling by Adjusting the Solid Acceptance Angle: a Starting Point to “ Three-Dimensional Imaging""" --- p.59 / Chapter 5.1 --- Introduction --- p.59 / Chapter 5.2 --- Theoretical Background --- p.60 / Chapter 5.2.1 --- Quantification of Intensity --- p.60 / Chapter 5.3 --- Experimental --- p.69 / Chapter 5.3.1 --- Operation --- p.69 / Chapter 5.3.2 --- Calibration of iris --- p.70 / Chapter 5.3.3 --- Novel depth profile by adjusting the solid acceptance angle --- p.71 / Chapter 5.4 --- Results and Discussions --- p.71 / Chapter 5.4.1 --- Depth Profiles --- p.71 / Chapter 5.4.2 --- "Concept of ""Three-Dimensional XPS Imaging""" --- p.72 / Chapter 5.5 --- Conclusions --- p.76 / Chapter Chapter 6 --- Correction to Quantitative X-ray Photoelectron Spectroscopy with Consideration of the Solid Acceptance Angle --- p.79 / Chapter 6.1 --- Introduction --- p.79 / Chapter 6.2 --- The effect of the solid acceptance angle --- p.80 / Chapter 6.3 --- Theoretical Background --- p.83 / Chapter 6.4 --- Results and Discussions --- p.87 / Chapter 6.4.1 --- Homogeneous Sample --- p.87 / Chapter 6.4.2 --- Layer structure --- p.90 / Chapter 6.4.3 --- Simulation plots and further investigation --- p.92 / Chapter 6.5 --- Conclusions --- p.101 / Chapter Chapter 7 --- Conclusion --- p.103 / Acknowledgment --- p.105 / References --- p.106

Yeung Shun-hin. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (leaves 52-54). / Abstracts in English and Chinese. / TITLE PAGE --- p.i / THESIS COMMITTEE --- p.ii / ABSTRACT (ENGLISH) --- p.iii / ABSTRACT (CHINESE) --- p.iv / ACKNOWLEDGEMENTS --- p.v / TABLES OF CONTENTS --- p.vi / LIST OF FIGURES --- p.viii / LIST OF TABLES --- p.x / Chapter Chapter 1 --- Introduction --- p.1 / Chapter Chapter 2 --- Computer-controlled Data Acquisition and Frequency Calibration System for a Ti: sapphire laser spectrometer --- p.3 / Chapter Section 2A --- Motivation and Overview --- p.3 / Chapter Section 2B --- The Hardware --- p.5 / Chapter Section 2C --- The Program --- p.12 / Chapter Section 2D --- Summary --- p.27 / Chapter Chapter 3 --- Cavity Enhanced Absorption Spectroscopy Using Phase-Sensitive Detection --- p.28 / Chapter Section 3A --- Motivation --- p.28 / Chapter Section 3B --- Cavity ring-down technique: the background --- p.29 / Chapter Section 3C --- Cavity enhanced absorption spectroscopy: a historical review --- p.34 / Chapter Section 3D --- Experimental Apparatus --- p.37 / Chapter Section 3E --- Results of Performance tests --- p.41 / Chapter Section 3F --- Applications --- p.45 / Chapter Section 3G --- Summary --- p.49 / Chapter Chapter 4 --- Concluding Remarks --- p.50 / REFERENCES --- p.52

"Ischemia is a condition of decreased tissue viability caused by a lack of perfusion, which prevents the delivery of oxygen and nutrients to biological tissue. Ischemia plays a major role in many clinical disorders, yet there are limited means by which tissue viability can be assessed. The long-term objective of this research is to develop a non-invasive or non-contact instrument for quantifying human tissue ischemia. Skeletal muscle ischemia is evaluated at this stage because skeletal muscle is easily accessible, its ischemia represents a clinical problem, and it can endure short periods of ischemia without suffering permanent injury. The ischemia monitor designed for this study is based on impedance spectroscopy, the measurement of tissue impedance at various frequencies. This study had three major goals. The first goal was to improve upon the design of the ischemia monitor to achieve optimal system performance in a clinical environment. Major considerations included electrode sterility, instrument mobility, and electrosurgical unit interference. The second goal was to collect both impedance and pH data from human subjects undergoing tourniquet surgeries, which induce skeletal muscle ischemia and result in changes of the tissue's pH and impedance. The average in recorded pH during ischemia was 0.0053 pH units/minute and the average change in Ro was -0.1481 Ohms/minute. The third goal was to develop a relationship between parameters of tissue impedance and pH utilizing neural networks. This goal was accomplished in three stages. First, the optimal neural network type for classifying impedance data and pH values was determined. Based on these results, the backpropagation neural network was utilized for all subsequent work. Then, the input parameters of the neural network were optimized using previously collected data. The number of inputs to the previously developed neural network were reduced by 35% (13/20) with a maximum of a 3% reduction in neural network performance. Finally, the neural network was trained and tested using human impedance and pH data. The network was able to correctly estimate tissue pH values with an average error of 0.0440 pH units. Through the course of this research the ischemia monitor based on impedance spectroscopy was improved, a methodology for the use of the instrument in the operating room was developed, and a preliminary relationship between parameters of impedance spectra and pH was established. The results of this research indicate the feasibility of the instrument to monitor both pH and impedance in a clinical setting. Additionally, it was demonstrated that impedance data collected non-invasively could be used to estimate the pH and level of ischemia in human skeletal muscle."

Photocopy of typescript. / Digitized by Kansas Correctional Industries

Intracellular protein-protein interactions (PPIs) play a vital role in many biological processes. Although they are viewed as of high biological interest they prove difficult to explore as potential targets for drug discovery. Numerous studies have shown α- helical peptides 'locked' in their respective bioactive structure can greatly increase their performance by increasing their target affinity, resistance to proteolysis as well as facilitating cellular uptake. A striking feature of literature to date is how few studies utilise different stapling techniques when developing inhibitors for PPIs. Current methods generally exploit ruthenium catalysed ring closing metathesis (RCM) or copper catalysed alkyne/azide click (CuAAC) chemistry to generate geometrically constrained peptides. Even though these methods have shown great potential they both share a fundamental limitation as the chemistry can only be employed on small synthetic peptides and cannot be extended to larger proteins. Thiol-ene coupling (TEC) chemistry (Chapter 1) which is often described as a 'click' reaction due to its fast reaction rates, high yields, wide functional group tolerance and insensitivity to ambient oxygen and water has the potential to solve this challenge. Thiol-ene chemistry was investigated as an alternative stapling strategy by employing the naturally occurring amino acid L-cysteine (Cys) as a source of the thiyl radical and L-homoallylglycine (Hag), a non-natural amino acid shown to act as a methionine surrogate in protein synthesis to act as a source of an alkene functionality to form a potentially expressible thioether tether in Chapter 2. However, due to unsatisfactory results from the intramolecular thiol-ene cyclisation at the molar concentrations required for peptide or protein modification, and a promising new lead, the closely related thiol-yne reaction was investigated as an alternative in Chapter 3. Using a small library of peptides (14 mers) derived from α-Synuclein (αSyn), a protein mainly found in the presynaptic terminals in the brain and is believed to be key to the pathological progress of Parkinson's disease, a successful macrocyclisation was achieved between the side chains of cysteine (Cys) and homopropargylglycine (Hpg). Although the vinyl-thioether tether did not confer any helical conformation on the stapled peptides, the results clearly demonstrate a potential route for the development of expressible staples. Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labelling (SDSL) of biomolecules has become a powerful tool for studying the structure and conformational dynamics of biomolecules. Typically, proteins are modified in a site-specific manner by utilising the side chains of cysteine residues to form disulphide bonds with spin active compounds, however, this strategy has its limitations. In Chapter 3 thiol-ene chemistry was investigated as an alternative biorthogonal method to spin label proteins and peptides. The newly synthesised sulfhydryl bearing nitroxide spin label was found to degrade upon exposure to radical promoting conditions, however, an alternative strategy was explored using more classical thiol-Michael chemistry to spin label dehydroalanine (Dha) modified peptides giving the desired spin labelled complex.

No description available.

Foram estudados através de espectroscopia vibracional, Raman e infravermelho, uma série de derivados do íon pentacianocobaltato(II), de fórmula geral [Co(CN)5-L-Co(CN)5]n-, onde L é H2C=CH2, H3COOC-C=C-COOCH3, C2H5COO-C=C-COOC2H5, SO2, O--2, O-2 ou NO2. Além desses Complexos, o íon dímero [Co2(CN)10]6- também foi objeto de estudo. No caso dos íons [Co(CN)5-L-Co(CN)5]n- os espectros vibracionais na região de estiramento CN são interpretados com base numa simetria C4v dos grupos Co(CN)5 isolados. A natureza das ligações C=N e das, ligações do ligante L para esses compostos é discutida com base nos resultados obtidos. / The vibrational spectra (Raman and infrared) of a series of compounds of general formula [Co(CN)5-L-Co(CN)5]n-, derived from the pentacianocobaltate(II) ion, where L is H2C=CH2, H3CCOO-C=C-COOCH3, C2H5COO-C=C-COOC2H5, NO2, SO2, O--2 or O-2, were studied. The dimer ion [Co2(CN)10]6- has also been subject of study. In the case of the [Co(CN)5-L-Co(CN)5]n- ions the vibrational spectra in the region of CN stretching vibrations were interpreted based on the C4v symmetry of the isolated Co(CN)5 groups. Characteristic frequencies of the ligand L and skeletal vibrations of Co(CN)5 group are tentatively assigned. The nature of C=N bonding and the structure of ligand L for these compounds are discussed on the basis of the obtained spectral results.