Photophysical and photochemical analysis and synthesis of biological imaging tools

Part I. Carbocations are traditionally thought to be closed-shell electrophiles featuring an empty orbital rich in p character. Unlike other atom-centered reactive intermediates such as nitrenes, carbenes, and nitrenium ions, which have one or more lone pairs, it is difficult to envision alternative electronic states for simple carbocations. However, some exceptions do exist, such as antiaromatic, substituted dicoordinated (aryl/vinyl) cations, and meta-donor-substituted benzylic cations, which adopt triplet ground states. Open-shell singlet and triplet “carbocations” may have distinct reactivity from typical closed-shell singlet carbocations and, if appropriately stabilized, lead to organic materials with interesting electronic and magnetic properties, such as spin switches and photocages. Photocages are light-removable protecting groups, which represent an important class of chemical tools. Photocages are useful by having a deactivating effect on the substrate to which they are covalently bonded, rendering the substrate “inactive” until exposed to light. Upon irradiation, the covalent bond is cleaved releasing the “active” substrate with precise spatiotemporal resolution. This highly controlled release makes photocages valued in biological systems. The next three chapters provide insight into the rational design and synthesis of new BODIPY-based photocages, that can absorb in the biological window (600 – 1000 nm). In Chapter 1, density functional theory computations indicate that when strong π donors are not placed in direct conjugation with benzylic-type cations, alternative diradical configurations that resemble non-Kekulé diradicals are possible. For certain donor-acceptor frameworks, an open-shell singlet configuration is the computed ground state for the cation, whereas for coumarin and xanthenyl cations substituted with strong donors, a triplet diradical configuration is the computed ground state. Changing the substituent nature and attachment location substantially alters the energy gaps between the different electronic configurations and can manipulate the computed ground state electronic configuration. There are few known examples of ground-state triplet carbocations, and, to our knowledge, no other examples of open-shell singlet carbocations. In Chapter 2, based on computational searches for good chromophores with low-energy diradical states, meso-substituted BODIPY dyes were synthesized which release acetic acid upon green light irradiation (\u3e500 nm). Compared to the popular o-nitrobenzyl systems, our photocages were found to have superior optical properties making them promising alternatives. The utility of these photocages in living S2 cells was demonstrated. In Chapter 3, the π electron conjugation of the meso-substituted BODIPY photocage was extended through the use of Knoevenagel condensation reactions. This extension resulted in a red-shift of the optical properties (\u3e600 nm) and allowed for cleavage of acetic acid within the biological window (600-1000 nm). Part II. Oxenium ions are reactive intermediates of formula R–O+, that are poorly understood. Previous computational and experimental work from our lab has allowed for better understanding these short-lived intermediates. The following chapters continue to add to this understanding by elucidating the electronic configuration, spectroscopic signatures, spin-selective reactivity, and lifetimes of these oxenium ions. In Chapter 4, the synthesis of p-biphenylhydroxylamine hydrochloride salt and the spectroscopic detection of p-biphenylyloxenium ion are described. Ultrafast LFP experiments on p-biphenylhydroxylamine suggested that photolysis leads to the p-biphenylyl radical as well as the p-biphenylyloxenium ion in differing electronic states. In Chapter 5, the synthesis of m-dimethylaminophenylhydroxylamine hydrochloride salt and the spectroscopic detection of m-dimethylaminophenyloxenium ion are described. Computations predict this oxenium ion to have a triplet ground state by 12 kcal/mol (B3LYP/cc-PVTZ). Product studies were performed for both photolysis and thermolysis as well as matrix isolation EPR studies. The matrix isolated EPR data gave strong evidence that the ground state of m-dimethylaminophenyloxenium ion being a triplet with indicative ΔMs = 2. Ultrafast LFP experiments on m-dimethylaminophenylhydroxylamine suggested that photolysis leads to a short-lived singlet m-dimethylaminophenyloxenium ion that quickly undergoes ISC to a triplet which later becomes a radical cation. Part III. Lignin is the second most abundant renewable organic compound next to cellulose, but is highly underutilized as a renewable source for liquid fuels and aromatic chemicals. Through the use of fast pyrolysis, lignin can be converted into bio-oil, which could later be used to make hydrocarbon fuels. Very little is known regarding the fundamental mechanisms of lignin pyrolysis, even though extensive research has been conducted. At the high temperatures necessary for pyrolysis, it is reasonable to think that radicals may play a mechanistic role. However, many radical species are short-lived and cannot be detected in their native form. In order to overcome this transient nature, spin-traps can be used. Spin-traps are molecules that react with radicals to form relatively stable radical adducts, which then can be studied to provide chemical composition and structural information. In Chapter 6, we investigated the pyrolysis of corn stover milled lignin at 500ðC using a Frontier Lab micro-pyrolyzer. In order to gain mechanistic insight into lignin pyrolysis, we passed the volatile pyrolysis products through a solution of the 5,5-dimethyl-1-pyrroline N-oxide (DMPO) spin-trap. We were able to detect the presence of three short-lived radical adducts that resulted from the pyrolysis using EPR and determined their molecular composition using LC-MS. Further studies, of additional lignin sources are currently being conducted for comparison