Colón Santos, Stephanie Marie (2019) Exploring the untargeted synthesis of prebiotically-plausible molecules. PhD thesis. https://theses.gla.ac.uk/75152/ Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] Exploring the Untargeted Synthesis of Prebiotically-Plausible Molecules A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy School of Chemistry College of Science and Engineering University of Glasgow Presented by Stephanie Marie Colón-Santos September 2019 Acknowledgements 3 Acknowledgements The work presented in this thesis was carried out between February 2016 and August 2019 in the group of Prof. Leroy Cronin in the School of Chemistry at the University of Glasgow. Through-out the years, I received the help and support of several group members. In particular, I would like to express my sincere gratitude to the following people: Prof Leroy Cronin, for taking me on as an intern in June 2015 and giving the opportunity to start a PhD in his research group. It has been a life-changing experience. Dr Geoffrey J. T. Cooper, for being a great team leader and providing excellent guidance during the writing process of my first-first author paper. Also for proofreading most of this thesis. Dr Andrew J. Surman, for teaching me about multiple analytical techniques during the first-part of my PhD and providing me with the essential skills for my research. Dr Irene Suarez-Marina, for her great help during my PhD and the overall savvy advice. Dr Laia Vila-Nadal, for help being a great role-model and my ‘big-sister’ away from home. Dr Dario Caramelli, Dr Vasilis Duros, Dr Eric Jannusson, Dr Davide Angelone, Andrius Bubliauskas, Manuel Kupper, Alex Hammer and Tom Goosens, for being more than colleagues and offering me their friendship during this experience. I will always keep our memories very close to my heart. Dr Rebecca Turk Macleod, Ms Liva Donina, Dr Jaroslaw Granda, Dr James Taylor, Dr Irene Suarez-Marina, Dr Sergio Martin, Dr Jessica Bame, Mr Hector Soria, Ms Sabrina Galinares, Dr Yousef Abul-Haija, Dr Ommid Anamimoghadam, Dr Jonathan Grizou, Dr Laurie Points and Dr Leanne Bloor for being awesome co-workers, making working hours much more enjoyable and always being up for a science chat. Jim McIver and Diana Castro-Spencer, for their endless help whenever I had technical problems and their unconditional kindness. Acknowledgements 4 Amanda McGarvey, for her administrative help and support. Also, I do not want to forget Cassandra Clarkson, Yaritza Santos and Paul Vincent Ferri. Although they are not Cronin group members, they made a genuine difference through the most challenging moments of the PhD. All the members of the Cronin Group, past and present, who have helped to make this experience an unforgettable one. Table of Contents 5 Table of Contents Acknowledgements ............................................................................................................... 3 Table of Contents ................................................................................................................. 5 Publications ........................................................................................................................... 8 Abbreviations ....................................................................................................................... 9 Abstract ............................................................................................................................... 10 1. Introduction Origins of Life: An open question ...................................................... 11 A (brief) history of the ‘Origins of Life’ field .................................................. 13 1.1.1 The philosophy of Life: Vitalism and Spontaneous Generation .................... 13 1.1.2 Darwinian evolution: A game-changer .......................................................... 14 1.1.3 Abiogenesis: The birth of Prebiotic Chemistry .............................................. 15 The cradle of life: A selection of geochemical scenarios .................................. 17 1.2.1 Warm-little pond ............................................................................................ 17 1.2.2 Hydrothermal-vents........................................................................................ 20 1.2.3 Water-soil interface (Mineral-clay hypothesis) ............................................. 21 Approaches to Prebiotic Chemistry ................................................................. 26 1.3.1 Autotrophic versus Heterotrophic Origins of Life ......................................... 27 One-pot synthesis of building blocks ................................................................ 32 1.4.1 Miller-Urey experiment: Amino acids ........................................................... 33 1.4.2 Formose Reaction: Sugars ............................................................................. 41 1.4.3 HCN and Formamide condensation: Nucleobases ......................................... 43 Systems Chemistry ............................................................................................. 46 Prebiotic mixtures: An analytical challenge ..................................................... 47 1.6.1 Preferred analytical techniques ...................................................................... 48 1.6.2 GC-MS ........................................................................................................... 49 1.6.3 LC-UV and HR-MS ....................................................................................... 53 1.6.4 FT-ICR-MS .................................................................................................... 57 1.6.5 Towards an untargeted approach ................................................................... 59 Table of Contents 6 Aims ..................................................................................................................................... 61 2. Results and Discussion ............................................................................................... 62 The Miller Urey experiment in a ‘Deuterium’ world ..................................... 62 2.1.1 Experimental setup ......................................................................................... 63 2.1.2 Gas-Chromatography coupled to Mass Spectrometry (GC-MS) ................... 65 2.1.3 HPLC-FLD ..................................................................................................... 71 2.1.4 Elemental analysis and SEM-EDS ................................................................. 74 2.1.5 Principal Component Analysis (PCA) ........................................................... 77 2.1.6 Section Summary ........................................................................................... 81 The Formose reaction in Formamide: A model system for prebiotic complex mixtures ........................................................................................................................... 83 2.2.1 Recursive cycles ............................................................................................. 85 2.2.2 UPLC-HRMS: An untargeted method ........................................................... 87 2.2.3 The Long Cycle ............................................................................................ 105 2.2.4 Non-Recursive control ................................................................................. 108 2.2.5 Reproducibility Assessment ......................................................................... 109 2.2.6 Comparison test: Formose reaction and Formamide condensation ............. 113 2.2.7 Feature Analysis ........................................................................................... 118 2.2.8 Section Summary ......................................................................................... 124 The Recursive Miller-Urey experiment ......................................................... 127 2.3.1 Recursive cycles ........................................................................................... 127 2.3.2 UPLC-MS/MS ............................................................................................. 128 2.3.3 Feature Analysis ........................................................................................... 131 2.3.4 1H –Nuclear Magnetic Resonance (1H-NMR) of the insoluble fraction ...... 141 2.3.5 Section summary .......................................................................................... 143 3. Conclusions and Future Work ................................................................................ 145 Miller-Urey: In a deuterium world ................................................................ 145 Recursive cycles of the Formose – Formamide reaction .............................. 146 The Recursive Miller-Urey Experiment........................................................