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I. Designing Brighter Fluorophores: a Computational and Spectroscopic Approach to Predicting Photophysical Properties of Hydrazone-Based Dyes Ii

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I. Designing Brighter Fluorophores: a Computational and Spectroscopic Approach to Predicting Photophysical Properties of Hydrazone-Based Dyes Ii University of Vermont ScholarWorks @ UVM Graduate College Dissertations and Theses Dissertations and Theses 2017 I. Designing Brighter Fluorophores: A Computational And Spectroscopic Approach To Predicting Photophysical Properties Of Hydrazone-Based Dyes Ii. Developing Spectroscopic Methods To Better Understand The Cofactors Of Metalloproteins Morgan Cousins University of Vermont Follow this and additional works at: https://scholarworks.uvm.edu/graddis Part of the Chemistry Commons Recommended Citation Cousins, Morgan, "I. Designing Brighter Fluorophores: A Computational And Spectroscopic Approach To Predicting Photophysical Properties Of Hydrazone-Based Dyes Ii. Developing Spectroscopic Methods To Better Understand The ofaC ctors Of Metalloproteins" (2017). Graduate College Dissertations and Theses. 787. https://scholarworks.uvm.edu/graddis/787 This Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks @ UVM. It has been accepted for inclusion in Graduate College Dissertations and Theses by an authorized administrator of ScholarWorks @ UVM. For more information, please contact [email protected]. I. DESIGNING BRIGHTER FLUOROPHORES: A COMPUTATIONAL AND SPECTROSCOPIC APPROACH TO PREDICTING PHOTOPHYSICAL PROPERTIES OF HYDRAZONE-BASED DYES II. DEVELOPING SPECTROSCOPIC METHODS TO BETTER UNDERSTAND THE COFACTORS OF METALLOPROTEINS A Dissertation Presented by Morgan E. Cousins to The Faculty of the Graduate College of The University of Vermont In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Specializing in Chemistry October, 2017 Defense Date: August 7, 2017 Dissertation Examination Committee: Matthew D. Liptak, Ph.D., Advisor Adrian Del Maestro, Ph.D., Chairperson Rory Waterman, Ph.D. Matthias Brewer, Ph.D. Cynthia J. Forehand, Ph.D., Dean of the Graduate College ABSTRACT Luminogens are molecules that emit light upon exposure to high-energy light, and fluorophores are one class of luminogens. Applications of fluorophores range from microviscosity sensors to light emitting diodes (LEDs), as well as biosensors, just to name a few. Many of these applications require the fluorophore to be in the aggregate or solid state. Some fluorophores become highly emissive in the aggregate state; these fluorophores are aggregation-induced emission (AIE) luminogens. Currently, very few quantum mechanical mechanisms have been proposed to describe the unique AIE behavior of luminogens. Boron difluorohydrazone (BODIHY) dyes are a new type of AIE fluorophore. The bright emission is from the S>1 excited state (“anomalous” emission) contrary to Kasha’s Rule. Thus, the mechanism Suppression of Kasha’s Rule (SOKR) was proposed to be responsible for the family of BODIHY dyes. We hypothesize that the SOKR mechanism can explain AIE as well as the anomalous emission of other fluorophores. New BODIHY derivatives (para-CO2H BODIHY, aluminum difluorohydrazone (ALDIHY), and para- nitro ALDIHY) were predicted to be bright anomalous fluorophores through density functional theory (DFT) and time-dependent DFT (TDDFT) investigations. In addition, a series of anomalous fluorophores were investigated to determine if their photophysical properties could be explained by the SOKR mechanism (azulene, 1,6-diphenyl-1,3,5- hexatriene, and zinc tetraphenylporphyrin). Finally, several triazolopyridinium and triazoloquinolinium dyes were computationally investigated by DFT and TDDFT calculations, and an accurate computational model for the large Stokes shifts of these dyes was developed. In conclusion, a better understanding of the photophysical properties through DFT and TDDFT modeling and spectroscopic investigation of hydrazone-based fluorophores has been achieved. In addition, the metal active sites and cofactors of metalloproteins were probed by optical spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and DFT modeling. In conjunction, these techniques can be used to elucidate the electronic structure responsible for the unique function of these metalloproteins. Specifically, a novel iron- sulfur cluster of a metalloprotein that may be involved in endospore formation of Clostridium difficile, CotA, was characterized by magnetic circular dichroism (MCD) spectroscopy. We propose that CotA contains a high-spin [4Fe-4S] cluster and a Rieske [2Fe-2S] cluster. It appears that the multimerization of the protein is related to the cluster conversion at the interface of monomeric subunits where two [2Fe-2S] clusters combine to form the [4Fe-4S] cluster. In addition, a putative cobalamin acquisition protein from Phaeodactylum tricornutum, CBA1, was not expressed at sufficient concentrations in Escherichia coli for spectroscopic investigation. Finally, a new technique was developed using cobalt-59 NMR spectroscopy to better understand the nucleophilic character of cobalt tetrapyrroles, such as cobalamin (vitamin B12), as biological cofactors as well as synthetic catalysts. New insight into the electronic structure provides valuable information related to the mechanism of these metalloproteins. CITATIONS Material from this dissertation chapter has been published in the following form: Qian, H., Cousins, M. E., Horak, E. H., Wakefield, A., Liptak, M. D., Aprahamian, I.. (2017). Suppression of Kasha's rule as a mechanism for fluorescent molecular rotors and aggregation-induced emission. Nat. Chem., 9, 83-97. ii TABLE OF CONTENTS Page LIST OF ABBREVIATIONS ......................................................................................... ix LIST OF TABLES ...................................................................................................... xxiii LIST OF FIGURES ................................................................................................. xxxvii LIST OF SCHEMES ................................................................................................... xlvi CHAPTER 1: INTRODUCTION .....................................................................................1 1.1. ELECTRONIC STRUCTURE DICTATES FUNCTION .....................................2 1.2. JABLONSKI DIAGRAM DESCRIBES LUMINESCENCE ................................3 1.3. APPLICATIONS OF FLUOROPHORES .............................................................5 1.4. INFLUENCE OF AGGREGATION ON EMISSION ..........................................8 1.5. DISTRIBUTION OF METALS IN BIOLOGY ...................................................10 1.6. DIVERSITY OF IRON-SULFUR CLUSTERS ...................................................13 1.7. FUNCTIONS OF COBALAMIN CONTAINING ENZYMES ..........................16 1.8. EXPERIMENTAL APPROACH TO CHARACTERIZE THE ELECTRONIC STRUCTURE OF HYDRAZONE-BASED FLUOROPHORES AND BIOINORGANIC COFACTORS ......................................................................21 1.9. CHAPTER 1 REFERENCES ...............................................................................23 iii CHAPTER 2: SUPPRESION OF KASHA’S RULE: A MECHANISM TO DESCRIBE THE ANOMALOUS EMISSION OF BORON DIFLUOROHYDRAZONE DYES ................................................................................26 2.1. INTRODUCTION ................................................................................................27 2.2. METHODS ...........................................................................................................36 2.3. RESULTS .............................................................................................................42 2.4. DISCUSSION .......................................................................................................62 2.5. CONCLUSIONS ..................................................................................................71 2.6. CHAPTER 2 REFERENCES ...............................................................................72 CHAPTER 3: IDENTIFYING NEW SOKR MOLECULES: DIHALIDE HYDRAZONE DERIVATIVES ....................................................................................74 3.1. INTRODUCTION ................................................................................................75 3.2. METHODS ...........................................................................................................79 3.3. RESULTS .............................................................................................................83 3.4. DISCUSSION .......................................................................................................89 3.5. CONCLUSIONS ..................................................................................................95 3.6. CHAPTER 3 REFERENCES ...............................................................................98 CHAPTER 4: DO OTHER ANOMALOUS FLUOROPHORES EXHIBIT AGGREGATION INDUCED EMISSION? ...................................................................99 4.1. INTRODUCTION ..............................................................................................100 iv 4.2. METHODS .........................................................................................................106 4.3. RESULTS ...........................................................................................................108 4.4. DISCUSSION .....................................................................................................112 4.5. CONCLUSIONS AND FUTURE WORK .........................................................117 4.6. CHAPTER 4 REFERENCES .............................................................................120
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