Applications of pulse shaping in the mid-infrared: Coherent control and two dimensional infrared spectroscopy of amyloid

The overarching goals of this dissertation are to improve two-dimensional infrared (2D IR) spectroscopy and apply it in better understanding fiber formation in the human islet amyloid polypeptide (hIAPP) and to coherently control ground state vibrational modes In addressing these goals we developed a mid-IR pulse shaper based on a Ge acousto-optic modulator (AOM) that enables us to generate time- and frequency-tailored mid-IR laser pulses. We learned that we can accurately produce mid-IR pulse pairs with predetermined temporal spacing and eliminate dispersion due to materials in the optical parametric amplifier (OPA), which are requirements for collecting standard 2D IR spectra. Furthermore, the Ge AOM-based pulse shaper makes it possible to rapidly acquire 2D IR spectra during hIAPP aggregation. By electronically scanning the first coherence time, we can quickly generate 2D IR spectra in a continuous fashion, which was not previously possible. We now have a better understanding of features in the 2D IR spectra of hIAPP and their relation to structural characteristics in the fully formed fibers based on experiments that employ isotope labels and a simple coupling model. We learned that structural markers such as frequency shifts, linewidths, and cross peak intensities change depending on the position of an isotope label within the hIAPP monomer.;Finally, towards controlling ground state vibrations, we use a closed loop optimization and phase tailoring to preferentially populate sequence bands of the T1u stretching mode in W(CO) 6. In order to better understand how population transfer over the duration of each optimized pulse is achieved, we systematically truncate our pulses and observe how each portion of the pulse alters population. Phase tailored pulses were used to eliminate the need for a master equation in extracting kinetics by preventing excitation to levels above that of which we are interested in extracting the population lifetime. We also employ polarization tailored pulses to selectively control population of the axial and equatorial modes in Mn(CO)5Br. We propose a mechanism for selective population based on the polarization dependence of higher order signals. Our approaches provide the groundwork for manipulating spectral features in decongesting and better understanding 2D IR spectroscopy.