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Proquest Disserststions THERMODYNAMIC PROPERTIES OF NUCLEIC ACID BASES AND NUCLEOSIDES UNDER HYDROTHERMAL CONDITIONS A Thesis Presented to The Faculty of Graduate Studies of The University of Guelph by VANESSA MANN In partial fulfilment of requirements for the degree of Master of Applied Science August, 2009 © Vanessa Mann, 2009 Library and Archives Bibliothèque et 1*1 Canada Archives Canada Published Heritage Direction du Branch Patrimoine de l'édition 395 Wellington Street 395, rue Wellington OttawaONK1A0N4 OttawaONK1A0N4 Canada Canada Your file Votre référence ISBN: 978-0-494-68602-7 Our file Notre référence ISBN: 978-0-494-68602-7 NOTICE: AVIS: The author has granted a non- L'auteur a accordé une licence non exclusive exclusive license allowing Library and permettant à la Bibliothèque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par télécommunication ou par l'Internet, prêter, telecommunication or on the Internet, distribuer et vendre des thèses partout dans le loan, distribute and sell theses monde, à des fins commerciales ou autres, sur worldwide, for commercial or non- support microforme, papier, électronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriété du droit d'auteur ownership and moral rights in this et des droits moraux qui protège cette thèse. Ni thesis. Neither the thesis nor la thèse ni des extraits substantiels de celle-ci substantial extracts from it may be ne doivent être imprimés ou autrement printed or otherwise reproduced reproduits sans son autorisation. without the author's permission. In compliance with the Canadian Conformément à la loi canadienne sur la Privacy Act some supporting forms protection de la vie privée, quelques may have been removed from this formulaires secondaires ont été enlevés de thesis. cette thèse. While these forms may be included Bien que ces formulaires aient inclus dans in the document page count, their la pagination, il n'y aura aucun contenu removal does not represent any loss manquant. of content from the thesis. 1+1 Canada ABSTRACT THERMODYNAMIC PROPERTIES OF NUCLEIC ACID BASES AND NUCLEOSIDES UNDER HYDROTHERMAL CONDITIONS Vanessa Lynn Mann Advisor: University of Guelph, 2009 Dr. P. R. Tremaine This is an investigation of thermodynamic properties of nucleic acid bases and nucleosides under hydrothermal conditions. Standard partial molar volumes have been determined for neutral nucleic acid bases and some nucleosides at temperatures between 15 0C and 90 0C using an Anton Parr DMA 5000 densitometer. Additionally, standard partial molar volumes of neutral uridine, cytidine, and thymidine were calculated from densities measured at temperatures up to 200 0C and pressures up to 6 bar using a custom- built platinum vibrating tube densitometer. Standard partial molar heat capacities were determined at temperatures up to 135 0C using a NDSC-III scanning nanocalorimeter. Standard partial molar properties of nucleic acid base and nucleoside non-electrolyte solutions become progressively more positive as the critical point is approached. Standard partial molar volumes and heat capacities for chloride salts of nucleic acid bases and nucleosides, BH+Cl"(aq) were also determined at temperatures between 15 0C and 90 0C. Partial molar properties of solutions of charged nucleic acid components become increasingly negative as the critical point is reached. These experimental results are in stark contrast with the previous assertions made by LaRowe and Helgeson (2006]. It was also observed that the standard partial molar properties of both neutral and ionic nucleosides had much larger, positive values than their corresponding nucleic acid bases. This difference was attributed to contributions of the ribose group to standard partial molar properties, and was modeled and used to estimate the standard partial molar properties of neutral and positively charged guanine in water. Additionally, the first ionization constant of adenosine was determined at a pressure of 95 bar and temperatures up to 175 0C using a platinum flow-through UV-visible cell. At near-ambient temperatures, measured ionization constants agreed well with values predicted by the Van't Hoff equation, but deviated from this model as temperature increased. The thermal stabilities of adenosine in acidic, neutral, formic acid buffered and phosphate buffered solutions were determined using the UV-visible cell as a stopped flow system at 95 bar between 150 0C and 250 0C. Adenosine formed decomposition products with overlapping spectra, and this necessitated factor analysis techniques to resolve different species. As temperature increased, the number of coloured decomposition products formed increased, indicating multiple decomposition pathways and steps. Above 225 0C, decomposition products were unstable, and decomposed into colourless products quickly. Spectral deconvolution of kinetic measurements using SpecFit/32© indicated that different reaction products were formed in the phosphate buffered system than the formic acid buffered system. It is believed that the phosphate buffered system produced a phosphate-adenosine complex that was unstable at ambient temperatures, and could not be isolated. ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. Tremarne, for his guidance and leadership on this project. I am especially grateful to Dr. Lilliana Trevani for all of her technical assistance and wisdom, both of which were invaluable contributions to my research. I am also thankful to all past and present members of the Tremaine group, especially Kristy and Melerin, for all of their science and non-science related support for my project. Over these last 26.5 years, I have received seemingly never-ending encouragement and support from my parents and older sister in my personal life as well as my academic career. I know that I could never have reached this point, nor would I be going on to complete my Ph.D., if they had not seen me through it. And finally, I would be truly remiss if I did not thank my husband, Jon. You've seen me through all the late nights and weekends of work, the frustration, the anger, and the good times in these last two years. Truth be told, this document wouldn't exist if I didn't have you in my life, and for this, and for so many other things, I will always be grateful. ? Table of Contents ACKNOWLEDGEMENTS i LISTOFFIGURES ? LISTOFTABLES x CHAPTERl 1 1.1 General Overview 1 1.2 Deoxyribonucleic Acid and Ribonucleic Acid Constituents 4 1.3 Biomolecules and their Precursors under Hydrothermal Conditions 7 1.3.1 The Nature of Hydrothermal Vents 7 1.3.2 A Prebiotic 'RNA World' 10 1.3.3 The Theory of the Origins of Life at Hydrothermal Vents 12 1.3.4 Abiotic Formation of Biomolecules under Hydrothermal Conditions ..13 1.4 Engineering Applications of Extremophiles and DNA Under Hydrothermal Conditions 14 1.5 Thermodynamics of Aqueous Solutions 17 1.5.1 Reaction Equilibria 17 1.5.2 Thermodynamic Relationships to Gibbs Free Energy 21 1.5.3 Apparent and Standard Partial Molar Properties of Aqueous Solutions21. 1.5.4 Standard Partial Molar Volumes 23 1.5.5 Heat Capacities 25 1.5.6 Extrapolating to Infinite Dilution 26 1.6 Equations of State for Standard Partial Molar Properties 29 1.6.1 The "Density" Model 29 1.6.2 Helgeson-Kirkham-Flowers (HKF) Equations of State 30 1.6.3 OLI Software 35 1.7 Hydrothermal UV-Visible Spectroscopy 36 1.7.1 Background 36 1.7.2 Developments in Hydrothermal UV-visible Spectroscopy 38 1.8 Methods of Kinetic Analysis 39 1.8.1 Chemical Reactions 39 1.8.2 Kinetic Measurement Techniques 41 ii 1.8.3 Data Analysis Al 1.9 Research Objectives 44 CHAPTER 2 46 2.1 Chemicals and Materials 46 2.2 Determination of Standard Partial Molar Properties 47 2.2.1 Density Measurements 47 2.3 Heat Capacity Measurements 57 2.4 UV-visible Spectroscopy 60 2.4.1 High Temperature Apparatus 60 2.5 Batch Reactions of Adenosine with Phosphates at Elevated Temperatures64 CHAPTER 3 66 3.1 Introduction 66 3.2 Standard Partial Molar Properties of Neutral and Positively Charged Nucleic Acid Bases and Nucleosides 70 3.2.1 Standard Partial Molar Volumes 70 3.2.2 Modeling Standard Partial Molar Volumes 72 3.2.3 Standard Partial Molar Heat Capacities 105 3.2.4 Modelling of Standard Partial Molar Heat Capacities 106 3.2.5 Comparison with Literature 131 3.2.6 Discussion 132 3.3 Functional Group Additivity Models 137 3.3.1 Introduction 137 3.3.2 Analysis of Ribose Contribution to Standard Partial Molar Properties138 3.3.3 Determination of the V20 of Guanine 149 3.3.4 Discussion 153 3.4 Standard Partial Molar Properties of Ionization 155 CHAPTER 4 163 4.1 Acid Ionization Constant from 25 to 175 0C 163 4.1.1 Introduction 163 4.1.2 Measurement Uncertainties 169 4.1.3 Comparisons with Literature Data 172 4.1.4 Equations of State 172 4.1.5 Discussion 177 in 4.2 The Kinetics of Adenosine Thermal Decomposition Under Hydrothermal Conditions 178 4.2.1 Decomposition Kinetics of Aqueous Adenosine Solutions from 150 to 250°C 180 4.2.2 Adenosine and Phosphate Reactions from 150 to 225 0C 195 4.2.3 Discussion 203 CHAPTER 5 206 5.1 Conclusions 206 5.2 Areas for Future Work 208 5.3 Engineering Applications 209 CHAPTER 6 211 CHAPTER 7 223 iv LIST OF FIGURES Figure 1.1: General Structure of Pyrimidine and Purine Bases 5 Figure 2.1: Schematic diagram of the high temperature densimeter 52 Figure 2.2: Partial molar
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