Description
- Abstract:
- Rydberg Fingerprint Spectroscopy (RFS) has been deftly applied to small molecules and shown exquisitely sensitive to global molecular structure. This has stimulated interest in its application to proteins. To assess the potential viability of RFS for analyzing proteins we begin by developing an understanding of the properties of Rydberg states in simple model systems of biomolecular constituents. In this thesis, we investigate the RFS of N,N-dimethylformamide (DMFA), to mimic the peptide backbone and N,N-dimethylphenethylamine (PENNA), and N,N-dimethylcyclohexethylamine (CENNA), to mimic pendant amino acid side chains. We observe the presence of overlapping Rydberg manifolds originating from near degenerate nO and π2 orbitals of DMFA. Using several different wavelengths for excitation we are able to explore the regions form the lowest valance transitions to the upper Rydberg manifold. PENNA and its hydrogenated counterpart, CENNA, have been chosen for their two separate functional groups tethered in close proximity, akin to the amino acid side chains in proteins. The differences between the electronic structures of the phenyl and cyclohexyl groups provide an interesting contrast to compare the Rydberg electron dynamics as a function of neighboring functional groups. After photo-excitation at the amine, we observe the time evolution of the PENNA conformer distribution through the time dependent shift in the Rydberg electron binding energy. These conformer dynamics are driven by the photo-initiated Coulumbic interaction of the positive charge center on the amine and the aromatic ring, forming an intramolecular hydrogen bond. Separately, we observe a biexponential decay kinetics of the 3s state that is indicative of a crossing from the Rydberg state to a dissociative σ* state. The photoexcitation process deposits a large amount of internal energy locally at the amine, which has to pass through the bottleneck of the ethyl linkage to be distributed throughout the molecular coordinates. The initial localization of internal energy extends the C-C bond of the ethyl linkage, depressing the energy of the σ* state and thereby allowing for electronic state crossing. The σ* state of CENNA is found to be higher in energy than in the PENNA system, effectively quenching this mechanism. Consequently, no biexponential kinetics are observed.
- Notes:
- Thesis (Ph.D. -- Brown University (2010)
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Citation
Bush, Joseph Caissie,
"Rydberg Fingerprint Spectroscopy on Biomolecular Model Systems"
(2010).
Chemistry Theses and Dissertations.
Brown Digital Repository. Brown University Library.
https://doi.org/10.7301/Z0R20ZKS
