| This dissertation describes the study of the ultrafast dynamics and structures of biomolecules in a condensed phase by multi-dimensional infrared spectroscopy. An ultrafast multi-dimensional infrared spectrometer is a powerful tool that can measure molecular structures and dynamics on ultrafast time scales. This dissertation reports extensive studies of the conformations of a model dipeptide, N-acetyl-L-prolinamide (AcProNH2) in deuterated chloroform (CDCl3), and of the interaction between the pentapeptide leucine-enkephalin (Lenk) and bilayered membranes (bicelles). Femtosecond multi-dimensional infrared spectroscopy, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations are the methods of choice for this investigation. In the AcProNH2 project, spectral features in the amide-I and -II regions were obtained by rephasing (R), non-rephasing (NR), and reverse photon echo (RPE) pulse sequences with two polarization conditions (0°, 0°, 0°, 0°) and (45°, -45°, 90°, 0°). Detailed comparison of DFT and MD results with 2D-IR spectra suggest the major conformer of AcProNH 2 in CDCl3 is close to the gas phase global minimum, the trans-C7 form, and the trans-PII conformer is possibly the 2nd dominant conformer.;Another project focused on the peptide-membrane interaction of Lenk with bicelles. For this project, 2D-IR spectroscopy has been extended to 3D-IR measurements to determine the spectral diffusion of a tyrosine side chain. Distinct spectral diffusion of a Tyr side chain for p-cresol in water, Lenk in water, and Lenk in bicelles were shown through 3D-IR spectra. This study revealed that ultrafast hydrogen-bonding dynamics of the Tyr side chain to water occurs on the time scale of ca. 1 ps and is common to all three systems. It further suggests that the Tyr side chain in bicelles is located at the water-membrane interface. This work demonstrated the Tyr side chain as a potential infrared probe to local environments. |
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