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Synthesis and Evaluation of Derivatives and Analogs of Xanthene Dyes Xiangyang Xu Louisiana State University and Agricultural and Mechanical College, [email protected]

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Synthesis and Evaluation of Derivatives and Analogs of Xanthene Dyes Xiangyang Xu Louisiana State University and Agricultural and Mechanical College, Xxu3@Lsu.Edu Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2007 Synthesis and Evaluation of Derivatives and Analogs of Xanthene Dyes Xiangyang Xu Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Chemistry Commons Recommended Citation Xu, Xiangyang, "Synthesis and Evaluation of Derivatives and Analogs of Xanthene Dyes" (2007). LSU Doctoral Dissertations. 2249. https://digitalcommons.lsu.edu/gradschool_dissertations/2249 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. SYNTHESIS AND EVALUATION OF DERIVATIVES AND ANALOGS OF XANTHENE DYES A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirement for the degree of Doctor of Philosophy in The Department of Chemistry By Xiangyang Xu B.E., Central South University, 1996 M.E., University of Science and Technology of China, 2002 August, 2007 ACKNOWLEDGMENTS First, I would like to express my sincere gratitude to my advisor, Dr. Robert M. Strongin, for his guidance, support, and encouragement. His inspiration and patience helped me to stay focused on my goals. I would also like to thank Dr. William Crowe, Dr. David Spivak, Dr. Robert Cook and Dr. Kenneth Rose being my committee members. I fully appreciate their patience and time reading my dissertation and giving valuable advices. Then, I would like to thank the members of the Dr. Strongin’s Research Group, from the past to the present, Dr. Jorge Escobedo, Dr. Oleksandr Rusin, Dr. Nadia St. Luce, Dr. Rolanda Johnson, Dr. Kyu Kwang Kim, Dr. Weihua Wang, Onur Alpturk, Youjun Yang, Shan Jiang, George Samoei, for their willingness to help me. I enjoyed the time we shared together in LSU. The acknowledgement would also go to Dr. Frank Fronczek, Dr. Dale Trelevean for their help on my research. Finally, to the rest of my friends and family, thank you for all your support and love. ii TABLE OF CONTENTS ACKNOWLEDGMENTS……………………………………………………………….ii LIST OF ABBREVIATIONS…………………………………………………..….……..vi ABSTRACT…………………………………………………………………...…………xi CHAPTER 1 INTRODUCTION……………………………………………….………1 1.1 Definition of Xanthene Dyes………………….………………………....1 1.2 Properties of Xanthene Dyes……………………………….…...……….1 1.2.1 Xanthene Dye Spectral Properties……………………………….1 1.2.2 Photochemical Properties of the Xanthene Dyes………………...6 1.3 Synthesis of Xanthene Dyes………….………….………………………13 1.4 Application of Some Xanthene Dyes ..………………………….……….17 1.5 References………………………………………………………..….…...18 CHAPTER 2 COLORIMETRIC AND FLUOROMETRIC DETECTION OF CYSTEINE AND HOMOCYSTEINE..………………………………..22 2.1 Background……………………………………………………………....22 2.1.1 Homocysteine……………………………………………………22 2.1.2 Cysteine…………………………………………………………..23 2.2 General Thiol Detection Methods ………………………………..……...24 2.3 Formation of N-thiazolidines ………….………………………………...26 2.4 Multistep Synthesis of Fluorescein Dialdehyde …………....……….…..27 2.5 Reimer-Tiemann Reaction and Its Applications ………………………...28 2.6 Results and Discussion…………………………………………………..30 2.7 Experimental……………………………………………………………..39 2.8 Conclusion..………………………………………………………..……41 2.9 References…………………………………………………………..……41 CHAPTER 3 SELECTIVE DETECTION OF CYSTEINE AND DEVELOPMENT OF NIR SENSOR……………………………………………………….…...44 PART I SELECTIVE DETECTION OF CYSTEINE .......................…...44 3.1 Background………... …………………………………………………....44 3.2 Synthesis of Mono- and Di- α,β-unsaturated Fluorescein Aldehydes…47 3.3 Results and Discussion…………………………………………………..47 3.3.1 Addition of Cysteine to Conjugated Aldehydes..………………..47 3.3.2 Selective Detection of Cysteine with Fluoresceine-Derived Conjugated Aldehydes……..…………………………………….50 3.4 Experimental………………………………………………………….….57 PART II SYNTHESIS AND CHARACTERIZATION OF NOVEL HEPTAMETHINE CYANINE DYES AND APPLICATION IN THE DETECTION OF CYSTEINE AND HOMOCYSTEINE…………..…..58 3.5 Introduction…. …………………………………………………..…58 iii 3.6 Results and Discussion…………………………………………………..59 3.7 Experimental……………………………………………………………..65 3.8 Conclusion……………………………………………………………….70 3.9 References………………………………………………………………..71 CHAPTER 4 A HYDROGEL FOR BIOMEDICAL APPLICATION…………………72 4.1 Introduction………………………………………………………………72 4.2 Results and Discussion…………………………………………………..72 4.3 Experimental……………………………………………………………..74 4.4 Future Work…...…………………………………………………………78 4.5 Conclusion……………………………………………………………..78 4.6 References………………………………………………………………..79 CHAPTER 5 NOVEL SYNTHESIS OF POLYHALOGENATED DIBENZO-P-DIOXINS………………………………………………....81 5.1 Background………………………………………………………………81 5.2 Results and Discussion…………………………………………………..84 5.3 Experimental……………………………………………………………..86 5.4 Conclusion...……………………………………………………………..88 5.5 References………………………………………………………………..88 APPENDIX A: CHARACTERIZATION DATA FOR COMPOUND 2.2…………..…..…90 B: CHARACTERIZATION DATA FOR COMPOUND 2.3………………….94 C: CHARACTERIZATION DATA FOR COMPOUND 3.1………………….98 D: CHARACTERIZATION DATA FOR COMPOUND 3.2…………….….101 E: MALDI MS OF REACTION MIXTURE OF COMPOUND 3.1 AND CYS………………………………………………………… ……………104 F: 1H NMR OF COMPOUND 3.13…………………………….…………....105 G: CHARACTERIZATION DATA FOR COMPOUND 3.14...…………….106 H: 1H NMR OF COMPOUND 3.18………………………...………………..109 I: 1H NMR OF COMPOUND 3.15……………………………...…………...110 J: CHARACTERIZATION DATA FOR COMPOUND 3.16……...…….….111 K: CHARACTERIZATION DATA FOR COMPOUND 3.19.……………...114 L: CHARACTERIZATION DATA FOR COMPOUND 3.20.……………...116 iv M: CHARACTERIZATION DATA FOR COMPOUND 3.7.….…………...118 N: CHARACTERIZATION DATA FOR COMPOUND 3.8.….…………...121 O: CHARACTERIZATION DATA FOR COMPOUND 3.9.…………….....124 P: CHARACTERIZATION DATA FOR COMPOUND 4.7.…………...…...127 Q: 1H NMR OF COMPOUND 4.8.………………………………...………...130 R: 1H NMR OF COMPOUND 4.6.…………………………………..……...131 S: CHARACTERIZATION DATA FOR COMPOUND 4.5.…………...…...132 T: CHARACTERIZATION DATA FOR COMPOUND 5.2.…………...…...134 U: CHARACTERIZATION DATA FOR COMPOUND 5.6…………...…...136 V: CHARACTERIZATION DATA FOR COMPOUND 5.7.…………...…..138 W: CHARACTERIZATION DATA FOR COMPOUND 5.8.…………..…..140 X: CRYSTALLOGRAPHIC DATA FOR COMPOUND 2.2………………..142 Y: CRYSTALLOGRAPHIC DATA FOR COMPOUND 2.1………………..153 Z: CRYSTALLOGRAPHIC DATA FOR COMPOUND 2.3………………..165 AA: CRYSTALLOGRAPHIC DATA FOR COMPOUND 3.7……………..178 BB: CRYSTALLOGRAPHIC DATA FOR COMPOUND 3.8……………...193 CC: CRYSTALLOGRAPHIC DATA FOR COMPOUND 3.9……………...211 DD: LETTERS OF PERMISSION…………………………………….……229 VITA……………………………………………………………………………………231 v LIST OF ABBREVIATIONS BBr3 Boron tribromide BHC Brominated hydrocarbon ºC Degrees Celsius CaH2 Calcium Hydride Cal. Calculated CDCl3 Dueterated Chloroform CHC Chlorinated hydrocarbon C6H5Cl Chlorobenzene CHCl3 Chloroform CH2Cl2 Dichloromethane CH3CN Acetonitrile CH3OD Dueterated Methanol CH3OH Methanol 13C NMR Carbon-13 Neclear Magnetic Resonance (CH3)4Si Tetramethyl silane CH3SO3H Methanesulfonic acid CO Carbon Monoxide Cys Cysteine DCFH 2’,7’-Dichlorodihydrofluorescein DCM Dichloromethane DDQ 2,3-Dichloro-5,6-dicyano-1,4-benzoquinone vi DHR 123 Dihydrorhodamine 123 DHR-6G Dihydrorhodamine 6G D2O Dueterium oxide DMACA 4-(Dimethylamino)-cinnamaldehyde DMF N-N-Dimethylformamide DMSO Dimethyl sulfoxide EtOAc Ethyl acetate Et2O Diethyl ether EtOH Ethanol FAB Fast Atom Bombardment FT-IR Fourier Transform Infrared g Grams h Hours HCL Hydrochloric acid HCN Hydrocyanic Acid Hcy Homocysteine HIV Human Immunodeficiency Virus H2O Water H2O2 Hydrogen Peroxide HPLC High-Performance Liquid Chromatography 1H NMR 1-d Proton Nuclear Magnetic Resonance HPF 6-hydroxy-9-phenyl-fluorone HRMS High-Resolution Mass Spectrometry vii H2SO4 Sulfuric Acid ISC Intersystem Crossing M Molar (moles/Liter) mBrB Monobromobimane mM Millimolar (mmoles/Liter) MgSO4 Magnesium Sulfate MALDI Matrix-Assisted Laser Desorption Ionization MeOH Methanol mg Milligrams mL Milliliters mmol Millimoles MS Mass Spectrometry MW Molecular Weight NaBH4 Sodium Borohydride NaOt-Bu Sodium tert-butoxide Na2CO3 Sodium Carbonate NaHCO3 Sodium Bicarbonate NaOH Sodium Hydroxide Na2SO4 Sodium Sulfate NBA N-Bromoacetamide NBD-F 4-Fluoro-7-Nitrobenzofurazan NIR Near-infrared NMR Nuclear Magnetic Resonance viii O2 Oxygen OH Hydroxide OPA O-phthalaldehyde ORTEP Oak Ridge Thermal Ellipsoid Plot PAAm Polyacrylamide PBDD Polybrominated-dibenzon-p-dioxin PCDD Polychlorinated dibenzo-p-dioxin PMMA Poly-methylmethacrylate ppm Parts Per Million PTZ Phenothiazene PXDD Polyhalogenated dibenzo-p-dioxin RDS Rate Determining Step Rf Ratio to Solvent Front ROS Reactive Oxygen Species rt Room Temperature TCDD 2,3,7,8-tetrachlorodibenzo-p-dioxin TCDF 2,3,7,8-tetrachlorodibenzofuran THF Tetrahydrofuran tHcy Total Homocysteine TLC Thin-Layer Chromatography µM Micromolar (micromoles/Liter) UV Ultraviolet UV-Vis Ultraviolet-Visible ix XDD Halogenated dibenzo-p-dioxin XHC Halogenated hydrocarbon ZnCl2 Zinc Chloride λ Wavelength x ABSTRACT Xanthene dyes are one of the oldest synthetic dyes. Fluorescein was first synthesized by von Baeyer in 1871. Since its discovery, it has been extensively studied. Fluorescein can exist as four different ionic forms (cationic form, neutral form, monoanionic form and dianionic form). Under physiological conditions (pH 7.4), fluorescein mainly exists as the dianionic form which grants it large quantum yield
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