Chemical and biochemical applications of vibrational spectroscopy
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Vibrational spectroscopy is a technique that probes a molecule’s vibrational modes via infrared absorption and Raman scattering, and is often used as a tool for characterization and/or functional group determination. Because infrared (IR) and Raman spectra are directly influenced by the bonds between atoms, these techniques have many other applications. Two applications of these techniques are presented herein. The current work is divided into two parts: the first half involves the chemical application of vibrational spectroscopy in determining molecular symmetry and structure, and the second part incorporates these techniques in monitoring protein-substrate binding. To demonstrate some of the chemical applications of vibrational spectroscopy, normal coordinate and vibrational analyses were performed on two silacyclobutane derivatives: 1,1-dimethylsilacylobutane (DMSCBane) and 1,1-dimethylsilacyclobut-2-ene (DMSCBene), aided by quantum chemical calculations. Additionally, for DMSCBane, the adjusted r0 structural parameters were determined by combining ab initio results with existing experimental data, whereas for DMSCBene, only predicted structural parameters have been reported. For the biochemical applications, a normal coordinate and vibrational analysis was first performed on the substrate, phosphoenolpyruvate (PEP) in a buffer solution, using data from Fourier-transform infrared (FTIR) spectroscopy with an attenuated total reflectance (ATR) accessory. This method was then used to monitor PEP binding to rabbit muscle pyruvate kinase (rM1-PYK) using IR difference spectroscopy. This work attempts to address deficits in previous studies of PEP/rM1-PYK binding by: 1) using a different approach to subtracting a reference spectrum to achieve an IR difference spectrum and; 2) collecting spectral replicates to determine the statistical relevance of vibrational frequency shifting of bands from bound versus unbound PEP.
Table of Contents
Vibrational analysis, structural parameters, and ab initio calculations of 1,1-dimethyl-1-silacyclobutane -- Vibrational analysis and ab initio calculations of 1,1-dimethyl-1-silacyclobut-2-ene -- Monitoring rabbit muscle pyruvate kinase allostery using fourier-transformi infrared spectroscopy
Ph.D. (Doctor of Philosophy)