Graduation Semester and Year
Spring 2026
Language
English
Document Type
Dissertation
Degree Name
Doctor of Philosophy in Chemistry
Department
Chemistry and Biochemistry
First Advisor
Joseph Buonomo
Second Advisor
Dr. Dong
Third Advisor
Dr. Jeon
Abstract
This thesis describes the development of synthetic and analytical approaches for the modification and study of biologically relevant carbohydrates. The work is organized into five chapters, progressing from chemical functionalization of complex sugars to the investigation of enzymatic transformations using advanced NMR techniques.
Chapter 1 examines carbohydrates as dynamic chemical systems, emphasizing how structural flexibility and solution-phase equilibria govern reactivity. Particular focus is placed on the C6 position of hexoses, where structural accessibility and reduced steric hindrance provide a unique handle for both enzymatic and synthetic modification.
Building on these principles, this chapter explores strategies to extend C6 reactivity into synthetic applications, including the development of minimally protected and chemoselective transformations. Special attention is given to trehalose-based systems and bioorthogonal “click”-type reactions, where selective functionalization enables probe development for biological imaging. These studies demonstrate that chemoselectivity can be achieved without extensive protecting group strategies by leveraging intrinsic substrate properties and reaction conditions. Collectively, this work establishes a framework for controlling carbohydrate reactivity through structural accessibility, providing a foundation for the synthetic and mechanistic studies presented in subsequent chapters.
Chapter 2 introduces a separate line of investigation involving the F420-dependent enzyme Cryar. This work focuses on the development of rapid, NMR-based kinetic methods to monitor enzymatic transformations of sugar substrates in real time. Using short acquisition ¹H NMR experiments, reactions were followed on the minute timescale, allowing direct observation of substrate consumption and product formation. Experimental design emphasized precise timing, including pre-acquisition baselines and controlled enzyme addition, to capture early-stage kinetics. In support of these studies, 13C-labeled glucose-6-phosphate was synthesized to capture time sensitive key transformations and facilitate tracking of specific carbon positions during enzymatic turnover. Analysis of spectral changes provided insight into possible intermediates and mechanistic pathways, including evidence consistent with open chain intermediates and enediol species.
Chapter 3 expands this enzymatic work to Nocardia FGD (Noca), enabling comparison between related F420-dependent systems. Differences in reactivity, rate, and substrate behavior were evaluated using the same NMR-based approach, allowing direct comparison across enzyme systems. The use of isotopically labeled substrates further supported mechanistic interpretation and improved confidence in peak assignments across experiments. These studies highlight both shared and distinct mechanistic features, contributing to a broader understanding of F420-mediated transformations. Together, Chapters 3 and 4 demonstrate the benefits of NMR spectroscopy for studying rapid enzymatic reactions that are difficult to capture using traditional analytical techniques.
Chapter 5 and 6 focuses on trehalose, a disaccharide central to bacterial cell wall structure and metabolism. This work explores selective modification strategies to introduce reactive functionality onto the trehalose scaffold, enabling downstream chemical transformations. In particular, trehalose derivatives were designed to undergo retro-Cope type reactions with hydroxylamine partners in the presence of strained alkynes such as dibenzocyclooctyne (DBCO). These studies evaluate reaction efficiency, regioselectivity, and stability of intermediates under aqueous and biologically relevant conditions. Analytical methods including ¹H NMR and LC-MS were used to monitor reaction progress and confirm product formation. This chapter establishes trehalose as a viable platform for bioorthogonal labeling and rapid “click-like” chemistry in bacterial systems.
Overall, this thesis integrates synthetic carbohydrate chemistry with advanced spectroscopic analysis to address challenges in both chemical modification and enzymatic reactivity. The work provides new insight into the functionalization of biologically relevant sugars and establishes experimental frameworks for studying fast, cofactor-dependent biochemical transformations.
Disciplines
Life Sciences
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Recommended Citation
Czapski, Desiree, "Design and Synthesis of Functionalized Carbohydrates for Bioorthogonal Reactivity and Phosphate Derivatization" (2026). Chemistry & Biochemistry Dissertations. 11.
https://mavmatrix.uta.edu/chemistry_dissertations2/11