Exploring the Urease Mechanism by Light Driven Uncaging of Urea Compounds Restricted; Files Only
Bell, Sarah (Spring 2024)
Published
Abstract
Discovering the mechanisms of the urea cycle has been a major focus in chemistry due to the positive environmental and biological impacts the discovery can provide. Additionally, further synthesis of novel “caged” compounds has impact in delayed drug delivery and time sensitive experiments. Ru(Bipy)2 is a valuable tool for caging compounds in order to photocontrol the release of substrates in a reaction. The synthesized caged urea compound contained a Ru(Bipy)2 complex with a chlorine ligand and urea ligand. Upon photolysis the caged compound was used to control the delivery of urea to urease. The reaction was then monitored to determine new insights into the catalytic mechanism of urease. The caged molecules were synthesized and characterized with mass spectrometry, IR, and transient absorbance spectroscopy upon irradiation with light. These experiments provided evidence that the novel caged urea compound was synthesized and remained caged until photolysis. After the development of the caged compound, the cryogenic fourier transform infrared (FTIR) was used to monitor the urea-urease reaction at increasing temperature from 47K to 87K. Jack Bean and Klebsiella Aerogenes Ureases were used to determine if there would be any differences between the mechanisms. We found evidence that the mechanisms are largely the same but have dependence on the catalytic rate of the species-specific urease. The aim of this study is to discover intermediates of the urea cycle and advance the improvement of caged compounds.
Table of Contents
Chapter 1: An Introduction to Urease and Caged Compounds
1.1 Overview of Urease
1.1.1 Motivation: Applications of Understanding the Urease Mechanism and Challenges
1.1.2 Insights into Urease Activity
1.2 Overview of Caged Compounds
1.2.1 Motivation: Applications of Synthesis of Caged Compounds
1.2.2 Use of Ru(Bipy)2 to Caged Urea
1.3 Scope and Aims
1.4 References
Chapter 2: Synthesis and characterization of Caged Urea Using Ru(Bipy)2
2.1 Introduction
2.2 Methodology
2.2.1 cis-dichlorobis(2 2'-bipyridine)ruthenium
2.2.2 cis-Ru(bipy)2PPh3
2.2.3 13C Caged Urea Synthesis
2.2.4 Sample Preparation of Caged Urea
2.2.5 Conditions for Room Temperature FTIR
2.3 Results and Discussion
2.3.1 Mass Spectroscopy of Caged Urea
2.3.2 NMR Analysis of 13C Caged Urea
2.3.3 FTIR uncaging Urea
2.3.4 Light Uncaging Transient Absorbance
2.4 References
Chapter 3: Using Cryogenic FTIR to Probe Urea-Urease Intermediates
3.1 Introduction
3.2 Methodology
3.2.1 Preparation of Jack Bean Urease
3.2.2 Preparation of KAU Urease
3.2.3 Preparation of Sample for Cryogenic FTIR
3.3 Results and Discussion
3.3.1 Jack Bean Urease FTIR
3.3.1 Inhibited Urease FTIR
3.3.2 KAU Urease FTIR
3.4 References
Chapter 4: Conclusions and Perspectives
4.1 Aim 1: Synthesis and Characterization of Caged Compound
4.2 Aim 2: Spectroscopic Characterization of Intermediates
4.3 Aim 3: Cryogenic FTIR of intermediates.
4.4 Implication and Future Directions
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File download under embargo until 24 May 2026 | 2024-04-23 18:11:54 -0400 | File download under embargo until 24 May 2026 |
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