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Gas Phase Acidity and Proton Affinity Studies of Organic GAS PHASE ACIDITY AND PROTON AFFINITY STUDIES OF ORGANIC SPECIES USING MASS SPECTROMETRY by MIN LIU A Dissertation submitted to the Graduate School-New Brunswick Rutgers, The State University of New Jersey in partial fulfillment of the requirements for the degree of Doctor of Philosophy Graduate Program in Chemistry and Chemical Biology written under the direction of Professor Jeehiun K. Lee and approved by ________________________ ________________________ ________________________ ________________________ New Brunswick, New Jersey [October, 2011] ABSTRACT OF THE DISSERTATION GAS PHASE ACIDITY AND PROTON AFFINITY STUDIES OF ORGANIC SPECIES USING MASS SPECTROMETRY By MIN LIU Dissertation Director: Professor Jeehiun K. Lee DNA damaged bases are linked to carcinogenesis, aging and cell death. One of our main focuses is to examine the intrinsic reactivity of normal and damaged nucleobases in order to find out how damaged bases are different from normal bases. 1,N6-ethenoadenine (eA) is one of the damaged nucleobases which can be excised by alkyladenine DNA glycosylase (AAG) in humans. We find that the N9-H of eA is more acidic than adenine and guanine, which indicates that AAG may cleave certain damaged nucleobases as anions and deprotonated damaged bases are better leaving groups than deprotonated adenine and guanine. Furthermore, differentiation of damaged from normal bases may be enhanced by the nonpolarity of the active site. In addition we find that the N9-H of O6- methylguanine (OMG) is less acidic than adenine and guanine. This result is consistent with the fact that OMG is not an AAG substrate. We also studied the thermochemical properties and tautomerism of normal pyrimidine bases cytosine and thymine. Another of our focuses is the study of gas phase acidity studies of organic silanols and some known hydrogen-bonding organocatalysts. It is generally accepted that silanols ii are more acidic than their carbon analogs, but we have found that the theoretical carbon diol analogs are actually more acidic than silicon diols depending on substitution and structure. Polarizability versus induction, gas phase versus solution phase, catalysis and molecular recognition are also discussed. We are also interested in the proton affinity and reactivity of N-heterocyclic carbenes (NHCs). Stable NHCs are widely used as novel ligands for transition-metal- catalyzed reactions. The dialkylimidazolium salts (protonated carbenes) are also an important class of ionic liquids. It has been found that the second generation of Grubbs metathesis catalysts, which contain NHCs, are more acitive than the first generation of catalysts, which contain tricyclohexyl phosphine (PCy3) only. More basic carbenes presumably will be more effective ligands. Therefore we are interested in the proton affinity of carbenes versus PCy3. We find that both dimethyl carbene and ethyl methyl carbene are more basic than PCy3. Proton-bound dimers of carbenes and PCy3 are also found to exhibit interesting reactivity. iii DEDICATION To my daughter Renee Tongyu Yang iv ACKNOWLEDGEMENTS I would like to express my sincere appreciation to my advisor, Dr. Jeehiun K. Lee, for her numerious help and guidance over these years. I would also like to thank Dr. Ralf Warmuth and Dr. Karsten Kroph-Jespersen in Chemistry and Chemical Biology Department, and Dr. Brian Buckley from Environmental & Occupational Health Sciences Institute, for serving on my committee and for their valuable time and helpful suggestions. Especially thank to Dr. Brian Buckley and Dr. Ill Yang in EOHSI of Rutgers for their precious instrument time. I would like to thank the previous and current members of Lee group: Su Pan, Xiaofeng Shi, Meng Xu, Xuejun Sun, Anna Michelson, Daisy Cardoso, James Lim, Mu Chen, Kai Wang, Sisi Zhang, Yuan Tian and Jorge Pavon for their friendship and help in both research and life. Many thanks to Dr. Alexei Ermakov for his incredible expertise in instrumentation. I also thank Dr. Laurence Romsted and Dr. Gene Hall for their helpful discussion. I am very grateful to my parents and sister for their unconditional support and love at every step of my life. At last, I thank to my dear husband Lin Yang for his love, patience and support. v TABLE OF CONTENTS ABSTRACT OF THE DISSERTATION .................................................................... ii DEDICATION .............................................................................................................. iv ACKNOWLEDGEMENTS .......................................................................................... v TABLE OF CONTENTS ............................................................................................. vi LIST OF FIGURES ....................................................................................................... x LIST OF TABLES ...................................................................................................... xiii 1.1 Overview ................................................................................................................... 1 1.1.1 Gas phase acidity and proton affinity of nucleobases .................................... 1 1.1.2 Gas phase acidity studies of organic silanols ................................................. 6 1.1.3 Gas phase proton affinity of N-heterocyclic carbenes (NHCs) ..................... 7 1.2 Instrumentation .......................................................................................................... 8 1.2.1 FTMS ............................................................................................................. 8 1.2.2 ESI and ion trap mass spectrometer ............................................................. 11 1.3 Methodology ............................................................................................................ 15 1.3.1 Bracketing method ....................................................................................... 15 1.3.2 Cooks Kinetic Method ................................................................................. 18 1.3.3 Computational method ................................................................................. 20 Chapter 2 The Acidity and Proton Affinity of the Damaged Base 1,N6- Ethenoadenine in the Gas Phase versus in Solution: Intrinsic Reactivity and Biological Implications ................................................................................................ 21 vi 2.1 Introduction ............................................................................................................. 21 2.2 Experimental ............................................................................................................ 24 2.3 Results ..................................................................................................................... 27 2.3.1 Computational results: tautomers ................................................................ 27 2.3.2 Computational results: acidity ..................................................................... 27 2.3.3 Computational results: proton affinity ......................................................... 28 2.3.4 Experimental results: acidity ........................................................................ 30 2.3.5 Experimental results: proton affinity ........................................................... 33 2.4 Biological Implications ........................................................................................... 40 2.5 Conclusions ............................................................................................................. 42 Chapter 3 The Gas-Phase Thermochemical Properties of the Damaged Base O6- Methylguanine versus Adenine and Guanine ........................................................... 43 3.1 Introduction ............................................................................................................. 43 3.2 Experimental ............................................................................................................ 44 3.3 Results ..................................................................................................................... 44 3.3.1 Computational results: tautomers ................................................................ 44 3.3.2 Computational results: acidities ................................................................... 45 3.3.3 Computational results: proton affinities ....................................................... 45 3.3.4 Experimental results: acidities ..................................................................... 46 3.3.5 Experimental results: proton affinities ......................................................... 48 3.4 Discussion ................................................................................................................ 49 3.4.1 O6-methylguanine (OMG): tautomers, acidities and proton affinities ......... 49 vii 3.4.2 Comparison of adenine and guanine properties with O6-methylguanine (OMG). .................................................................................................................. 51 3.5 Conclusions ............................................................................................................. 57 Chapter 4 The Gas-Phase Thermochemical Properties of Pyrimidine Nucleobases .......................................................................................................................................... 60 4.1 Introduction ............................................................................................................
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