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A theoretical investigation on the role of hydrogen bonding in the degradation and photodynamics of small organic molecules: a dissertation in Chemistry and Biochemistry
Dissertation   Open access

A theoretical investigation on the role of hydrogen bonding in the degradation and photodynamics of small organic molecules: a dissertation in Chemistry and Biochemistry

Michael Dave Pogoy Barquilla
Doctor of Philosophy (PHD), University of Massachusetts Dartmouth
2024
DOI:
https://doi.org/10.62791/2001

Abstract

Hydrogen bonding plays a vital role in nature due to its unique properties that influence the structure and behavior of molecules in biological and chemical systems. Keto acids and phenolic analogs, for example, are heavily governed by hydrogen bonding. Changes in hydrogen bonding on keto-acids dictate the atmospheric aerosol cycling mechanism, while intramolecular hydrogen bonding in phenolic analogs impedes the ultrafast relaxation, reducing the photoprotection of proteins. However, the complete description of the photodegradation mechanisms of these two is obscured by conflicting product ratios and excited state lifetimes in experiments. Further, hydrogen bond strength depends on charge distribution and orbital interaction, which vary between gas and aqueous environments and the excited state, adding to the complexity. Theoretical simulations bridge the gaps in describing the mechanisms of photoinduced reactions and relaxations not fully characterized by experiments. To understand the role of hydrogen bonding in the two systems, this work performed an in-depth theoretical investigation using high-level quantum mechanical methods and nonadiabatic dynamic simulations. The models used are pyruvic acid (PA) for atmospheric keto-acids and o-fluorophenol for phenolic analogs. Results revealed that PA undergoes different degradation mechanisms in gas and aqueous phase. In gas phase, hydrogen bonding aided the initial proton transfer in multiple degradation channels, leading to faster acetaldehyde production. In aqueous phase, a new intermediate is found while all hydrogen bonding is weakened, leading to slower rates. In the excited state, decarboxylation and Norrish type bond cleavage are limited by the ultrafast relaxation within the Franck-Condon region due to weakened hydrogen bonding. On the other hand, o-fluorophenol’s hydrogen dissociation relaxation was impeded by competing butterfly decay modes, which retained their hydrogen bonding. These insights underscore the role of hydrogen bonding in atmospheric keto-acid chemistry, which impacts aerosol formation, and in aromatic excited state processes, which have broader applications in material science.
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Barquilla M.D.P. CAS PhD Dissertation 202429.38 MBDownloadView
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