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Photoaffinity Labeling Strategies Using Purine Nucleic Acid Bases

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Photoaffinity Labeling Strategies Using Purine Nucleic Acid Bases PHOTOAFFINITY LABELING STRATEGIES USING PURINE NUCLEIC ACID BASES Denis I. Nilov A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2011 Committee: Dr. R. Marshall Wilson, Advisor Dr. Robert M. McKay Graduate Faculty Representative Dr. Thomas H. Kinstle Dr. Alexander N. Tarnovsky ii ABSTRACT Dr. R. Marshall Wilson, Advisor. Photodecomposition of 8-azidoadenosine (24) and 8-azidoinosine (30) has been studied by ultrafast transient absorption spectroscopy methods in different solvents. The formation of two types of intermediates has been proposed for photodecomposition of 24 and 30: the diiminoquinone 25 for 24 with an EDG on the purine ring, an iminonitriles 26 for 24-H, and 38 for 30 in the absence of an EDG on the purine ring. Thus, nitrenes 31, which is formed from azide 24, undergoes proton reallocation to form iminoquinone 25. Iminoquinone 25 undergoes nucleophilic attack forming C2-adducts 33-Nuc, which aromatizes to 34-Nuc. Nitrenes 31-H and 31Bz5 afford to ring-opened iminonitriles 26-H and 26Bz5, respectively. Nucleophilic attack to iminonitrile 26-H leads to the formation the same product as C2-adducts 33-Nuc, which aromatizes. Azide 30 forms nitrene 36 which exclusively to rearranged to iminonitrile 38. Iminonitrile 38Ac3 displays the spectroscopic behavior similar to 26-H in the μs-ms time domains. A ring destruction product 35, 8-aminoadenosine, and adducts 34-IM and 34-OH have been isolated. Small amounts of dimer-like structures and other products have been detected, but have not been fully identified. The azide 39 has been synthesized for the first time and its photodecomposition has been studied. It has been proposed that in protic solvents a photolysis of azide 39 leads to singlet nitrene 53s, which undergoes the proton transfer from N7 to N6 through the solvent-bridged transition and forms iminoquinone 5. In aprotic media, singlet nitrene 53s undergoes ISC to triple nitrene 53t. Nucleophilic attack on iminoquinone 5 leads to the formation of C2-adducts, such as 56, that undergo aromatization to corresponding adducts 55-Nuc. Imidazole adduct 8 and iii product 2 and 3 have been isolated and characterized from the preparative irradiation of azide 39. Additionally, some amounts of other photodecomposition products have been detected, but have not been fully identified. Assignments of important intermediates based on experimental data have been supported by quantum chemical calculations using TD-DFT, CASSCF and CASSP2 methodologies. Azide 39 has been proposed as a candidate for a PAL reagent in biochemical studies of NA-protein and NA-NA interactions. iv ACKNOWLEDGMENTS At the beginning, I would like to thank my adviser, Professor R. Marshall Wilson. I am very grateful for sharing his knowledge, his support, encouragement, and guidance. I want to express my appreciation Professor Alexander N. Tarnovsky for the great collaboration. The discussions and suggestions that he proved were highly useful. I thank Kanykey Karabaeva and Andrey Mereshenko for acquisition of femtosecond spectroscopic data. Also, I would like to thank Maxim Panov for acquisition of femtosecond spectroscopic data and his help in quantum chemical calculations. I am very thankful to Professor Phil Castellano for opportunity to use instrumentation in his laboratories and Valentina Prusakova for her help in study of nanosecond spectroscopy technique. I thank Professor Massimo Olivucci and Elena Laricheva for their helpful advices in quantum chemistry calculations. I am very grateful to Professor Thomas H. Kinstle for his help and support during all this period. Also, I am very thankful for his sharing of knowledge of synthetic organic chemistry. I thank my committee member Professor Robert Michael McKay for his time and patience. I am grateful to Dr. Jedrzej Romanowicz and Dr. Larry Sallens for their help with mass spectroscopy and to Dr. D. Y.Chen for his help with NMR experiments. I thank Dr. Pavel Kucheryavy and Ekaterina Mirzakulova for their help in electrochemistry experiments. I also would like to thank personnel of Ohio Supercomputer Center for a possibility to support experimental data with theoretical calculations. v I was pleased to work in laboratory with members of our research group Alexei Shamaev, and Kanykey Karabaeva. Also, I am grateful to Dr. Dmitry Komarov, and Dr. Valentyna Voskresenska, and Dr. Sergey Voskresensky. I would like to thank them for maintaining a productive and friendly atmosphere. Finally, I would like to express my special gratitude to people who permanently supported me. I thank my dear friends, especially, Armen Ilikchyan, Alexander Krylov, Yuri Strezhik, and Anna Parinova for their permanent encouragement, comprehension, and friendship. I thank my dear parents for their love and support through all time. vi TABLE OF CONTENTS Page CHAPTER I. BACKGROUND......................................................................................... 1 1.1. Photoaffinity Labeling (PAL) ......................................................................... 1 1.2. Oxidation of Purine Bases via Formation of Quinoidal and Iminoquinoidal Intermediates.......................................................................... 5 1.3. Photochemistry of Aromatic Azide ................................................................. 10 1.4. References ...................................................................................................... 19 CHAPTER II. EXPERIMENTAL METHODS ................................................................. 30 2.1. Liquid Chromatography.................................................................................. 30 2.2. UV-VIS Absorption Spectroscopy .................................................................. 30 2.3. IR Spectroscopy.............................................................................................. 30 2.4. Mass Spectrometry ......................................................................................... 31 2.5. NMR Spectroscopy......................................................................................... 31 2.6. Femtosecond UV-VIS Time Resolved Absorption Spectroscopy .................... 31 2.7. Nanosecond UV-VIS Time Resolved Absorption Spectroscopy...................... 33 2.8. Quantum Chemistry Calculations.................................................................... 34 2.9. References ...................................................................................................... 34 CHAPTER III. PHOTOCHEMISTRY OF 8-AZIDOADENOSINE AND 8-AZIDOINOSINE.................................................................................................. 37 3.1. Introduction .................................................................................................... 37 3.2. Photochemical Studies of 8-Azidoadenosine (24)............................................ 39 3.3. Synthesis and irradiation of 8-Azidoadenosine (24), vii 8-Azidoinosine (30), and Their Derivatives ........................................................... 54 3.4. References ...................................................................................................... 60 CHAPTER IV. The Photochemistry of 6-azido-8-oxo-7,9-dihydropurine (39) .................. 62 4.1. Introduction .................................................................................................... 62 4.2. Chemical Generation of Iminoquinone 5 via oxidation of 8-oxoadenosine (2). 64 4.3. Photochemical Studies of 6-Azido-8-oxo-7,9-dihydropurinoriboside (39)....... 68 4.4. Conclusions .................................................................................................... 78 4.5. Synthesis of 6-azido-7,9-dihydro-8-oxopurine (39) and derivatives................. 78 4.6. References ...................................................................................................... 85 CONCLUSIONS ....................................................................................................... 87 SUPPLEMENTAL INFORMATION. HRMS SPECTRA. 1H AND 13C NMR SPECTRA. 88 viii LIST OF SCHEMES Scheme Page 1.1. Generally used PAL agents and their putative mechanisms. ................................... 3 1.2. Stepwise oxidation of guanosine............................................................................ 7 1.3. Oxidation of 8-oxopurines via formation of quinones and iminoquinones of purines and regioselectivity of nucleophile attack. ............................................. 8 1.4. Chemical oxidation of 8-oxoA (2) and 8-oxoI (3). ................................................. 9 1.5. The donation of electron from aromatic ring system to p-π orbital of nitrene 11..... 12 1.6. Mechanism for photolysis of phenylazide. ............................................................. 13 1.7. Formation of products from benzazirine 12 and dehydroazepine 13. ...................... 14 1.8. Dimerization and reduction of triplet nitrene 11t.................................................... 15 1.9. The chemistry of a fluorosubstitued aryl azide. ...................................................... 15 1.10. Photolysis of p-(N,N-diethylamino)phenylazide..................................................... 17 1.11. The chemistry of nitrenium ions. ........................................................................... 18 1.12. Photodecomposition of 21. ...................................................................................
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