Degree Type


Date of Award


Degree Name

Doctor of Philosophy



First Advisor

Arthur H. Winter


Part I. Photocages, which are light cleavable protecting groups, are an important class of chemical tools that allow light to unmask bioactive substrates with precise spatiotemporal resolution in biological microenvironments. Due to their effectiveness in biological systems, it has become increasingly important to find logically designed photocages that can cleave under visible light and Near IR conditions, wavelengths with minimal phototoxicity and increased tissue penetration compared to ultraviolet light. The scope of this research is to both rationally design and synthesize a new class of photocage based on the BODIPY moiety, as well as to modify these photocages to absorb in region of the biological window (600-1000 nm), where tissues have maximal transparency.

In chapter 1, photocages derived from meso-substituted BODIPY dyes were synthesized that release acetic acid when irradiated with green wavelengths (>500 nm). The structures of the photocages were derived by computationally searching for carbocations with low-energy diradical states as a possible indicator of nearby productive conical intersections. These photocages were found to have superior optical properties than the popular o-nitrobenzyl systems, which make them promising alternatives. The utility of these photocages in living cells was successfully demonstrated by our collaborators (Prof. Emily Smith and Aleem Syed) in cultured S2 cells.

In Chapter 2, Knoevenagel type reactions were used to extend the π electron conjugation of the aromatic rings of the BODIPY photocages. This extended conjugation of these BODIPY photocages resulted in a bathochromic shift in absorbance towards red light (>600 nm) and allows cleavage using wavelengths in the biological window.

Part II. Self-immolative linkers can be used to trigger the release of an important cargo molecule like a drug or a biomolecule. A variety of trigger stimulants including light, chemo and enzyme are known in literature. However, there is a need for new linker units which would have fast and controllable kinetics of cargo release. During my research, I identified improved self-immolative linker units based on aryl phthalate esters with a modular design, which can tolerate a range of different trigger and cargo units.

In Chapter 3, new types of self-immolative linkers based on the phenyl hydrogen phthalate system were synthesized. The fast kinetic rate for the hydrolysis of phenyl hydrogen phthalate system and the resulting benign byproducts promise a robust self-immolative linker system that can be used in biological systems. The linker system was shown to release phenol based cargo molecules including phenol and coumarin dyes upon cleavage by a fluoride sensitive trigger. This type of linker can also be potentially used as an efficient fluoride sensor.

In Chapter 4, the scope of self-immolative linkers based on phenyl hydrogen phthalate system was extended. Light and peroxide sensitive triggers were incorporated into the linker system. Coumarin based cargo molecules were used as reporter molecules and the increase in their fluorescence after release was monitored. The light-sensitive aryl phthalate ester was further demonstrated as a pro-fluorophore in cultured S2 cells.

Copyright Owner

Pratik Pran Goswami



File Format


File Size

153 pages