Modeling the Molecular Spectra of Selected Peptides and Development of an Optical Trapping Raman System

The objective in this thesis is to study the structure of peptides using molecular spectroscopy. Molecular spectroscopy, both vibrational and electronic, can be used as a sensitive tool to study molecular structure. Since it is an inherently low resolution method, theoretical calculations are essential for a complete understanding of vibrational and electronic spectra. The first part of this thesis contains quantum chemical calculations of the molecular spectra of several small peptide systems with different secondary structures. Optical trapping is a method that allows for the manipulation of sub-micron scale objects using tightly focused laser light. Raman spectroscopy, which is sensitive to molecular vibrations also requires intense laser light. Combined with optical tweezing, Raman spectroscopy can prove to be a very powerful tool to study small sample volumes and probe single living cells. In the second part of this thesis, I detail the construction an such an instrument, an optical trapping Raman spectrometer (OTRS). Our OTRS can measure Raman spectra from sub micron systems while at the same time quantifying the mechanical forces that are acting upon them. Thus the OTRS can give insight into the relationship between mechanical forces acting upon cells and their molecular structure.