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Ultrafast and single-molecule studies in non-equilibrium chemical dynamics
by Nome, Rene A., PhD, THE UNIVERSITY OF CHICAGO, 2007, 0 pages; 3273051
 

Abstract: In part I of this thesis, field-resolved approaches for studying solute and solvent dynamics on the femtosecond timescale are discussed. The implementation of spectral interferometry for full electric field-resolved studies and its application to linear pulse propagation in optically dense systems in the mid-infrared spectral region is presented. Electric field-resolved transient grating measurements are used to distinguish the four-wave mixing signal emission times form a resonant solute and a non-resonant solvent. The two components of the solution (i.e., solute and solvent) emit signal fields at different times with respect to the arrival of the probe pulse to the sample. This separability of responses is a general phenomenon that is particularly useful for studying weakly absorbing solute dynamics in polarizable solvents. Electric fields of coherent Raman signals are resolved with sensitivity for high-frequency vibrational resonances. The C-H stretching modes of cyclohexane and benzene are studied for two polarization conditions. The temporal profiles of signal fields for cyclohexane exhibit a low-frequency recurrence due to the interference between the signals associated with the symmetric and asymmetric C-H stretching modes. In contrast, the electronically nonresonant polarizability response of benzene gives rise to a significant broadband signal component in addition to that associated with its C-H vibrational resonance. Part II integrates experimental and theoretical non-equilibrium techniques to map energy landscapes along well-defined pull-axis specific coordinates to elucidate mechanisms of protein unfolding. Single-molecule force-extension experiments along two different axes of photoactive yellow protein (PYP) combined with non-equilibrium statistical mechanical analysis and simulation reveal anisotropy in protein unfolding. Steered MD (SMD) simulations and free-energy curves constructed from the experimental results reveal that unfolding along one axis exhibits a transition-state-like feature where six hydrogen bonds break simultaneously with weak interactions observed during further unfolding. The other axis exhibits a constant force profile indicative of a non-cooperative transition, with enthalpic interactions being broken throughout the unfolding process. Striking qualitative agreement was found between the force-extension curves derived from SMD calculations and the free energy curves obtained from Jarzynski analysis of the experimental data. Our findings challenge the notion that cooperative unfolding is a universal feature in protein stability.

 
Advisor: Scherer, Norbert F.
School: THE UNIVERSITY OF CHICAGO
Source: DAI-B 68/08, p. 5259, Feb 2008
Source Type: PhD
Subjects: Chemistry
Publication Number: 3273051
     
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