Studies on the Prebiotic Origin of 2-Deoxy-D-ribose Andrew Mark Steer Doctor of Philosophy University of York Chemistry August 2017 Abstract DNA is an important biological structure necessary for cell proliferation. The origins of cell- like structures and the building blocks of DNA are therefore also of great concern. As of yet the prebiotic origin of 2-deoxy-D-ribose, the sugar of DNA, has no satisfactory explanation. This research attempts to provide a possible explanation to the chemical origin of 2-deoxy- D-ribose via an aldol reaction between acetaldehyde 1 and D-glyceraldehyde D-2 (Error! Reference source not found.). The sugar mixture is trapped with N,N-diphenylhydrazine 3 for ease of purification and characterisation. The reaction is promoted by amino acids, amino esters and amino nitriles consistently giving selectivities in favour of 2-deoxy-D- ribose. This is the first example of an amino nitrile promoted reaction. Potential prebiotic synthesis of 2-deoxy-D-ribose and subsequent trapping with N,N-diphenyl hydrazine 3. The research is developed further by exploring the formation of 2-deoxy-D-ribose in a “protocell” environment – a primitive cell. Here we suggest that primitive cells may have been simple hydrogel systems. A discussion of the characterisation and catalytic ability of small peptide-based supramolecular structures is included. ii Contents Abstract ............................................................................................................................ ii Contents .......................................................................................................................... iii List of Figures .................................................................................................................. v List of Schemes ............................................................................................................ viii List of Tables ................................................................................................................... x Acknowledgements ....................................................................................................... xii Declaration .................................................................................................................... xiii 1. Introduction ............................................................................................................... 1 1.1. The Origin of Life and the RNA World hypothesis ................................................ 1 1.2. The Origin of Sugars............................................................................................ 6 1.3. Prebiotic Relevance of Amino Acids .................................................................... 8 1.4. Amino acids as catalysts in aldol reactions ........................................................ 15 1.5. Organocatalysis in water ................................................................................... 20 1.6. Peptides in organocatalysis ............................................................................... 30 1.7. Amino acid-catalysed sugar chemistry in a prebiotic scenario ........................... 34 1.8. Amplification of a Small Enantiomeric Excess.................................................... 43 1.9. Approaches to 2-Deoxyribose ............................................................................ 48 1.10. Conclusions and Research Objectives ........................................................... 51 2. A Prebiotic Route to 2-Deoxy-D-Ribose ................................................................ 53 2..1. Initial experimental design ................................................................................. 53 1. Synthesis of Standards and Catalysts ................................................................... 56 2. Results of the Initial reaction trials ......................................................................... 61 3. N, N-Diphenyl hydrazine trap ................................................................................ 67 4. Conclusion ............................................................................................................ 75 3. Amino nitriles – possible progenitors to amino acids ......................................... 76 3.1. Evidence for amino nitriles as prebiotic molecules ............................................. 76 3.2. Synthesis of amino nitriles ................................................................................. 79 3.3. Amino nitriles as potential catalysts ................................................................... 83 3.4. Prebiotic formation of glyceraldehyde ................................................................ 87 3.5. Racemic glyceraldehyde .................................................................................... 91 3.6. One pot synthesis of 2-deoxyribose ................................................................... 96 3.7. Conclusions ..................................................................................................... 103 4. Prebiotic Protocells .............................................................................................. 105 4.1. A Protocell Environment .................................................................................. 105 4.2. Proof of concept using agarose ....................................................................... 111 iii 4.3. Prebiotic protocells based on dipeptide amphiphile hydrogels ......................... 117 4.4. Conclusions ..................................................................................................... 130 5. Further investigations into hydrogel catalysis ................................................... 131 5.1. A tripeptide hydrogel candidate ....................................................................... 131 5.2. Supramolecular structures of a tripeptide amide .............................................. 137 5.3. Evidence of Micelle Aggregation ...................................................................... 140 5.4. Changing the amino acid sequence ................................................................. 147 5.5. Single amino amides for supramolecular catalysis ........................................... 149 5.6. Conclusions ..................................................................................................... 156 6. Experimental ......................................................................................................... 157 Abbreviations ............................................................................................................... 225 References ................................................................................................................... 228 iv List of Figures Figure 1.1. Central dogma of molecular biology. .................................................................. 1 Figure 1.2. The processes of transcription and translation that occur within a mammalian cell. ....................................................................................................................................... 2 Figure 1.3. Miller-Urey experimental set-up and amino acids synthesised. Reprinted with permission from J. Am .Chem. Soc., 1995, 77, 2351. Copyright 2017 American Chemical Society. ................................................................................................................................. 9 Figure 1.4. Five methyl-α-amino acids found in fragments of the Murchison meteorite. ...... 13 Figure 1.5. Proposed transition states leading to Si-facial attack in the L-histidine L-81 catalysed aldol reaction.67 ................................................................................................... 27 Figure 1.6. Catalyst 86 and relative transition state proposed by Pedatella et al.71 ............. 29 Figure 1.7. Proline derived catalyst 87 synthesised by Lipshutz and Ghorai.72 ................... 30 Figure 1.8. Conversion of amino nitriles to amino amides using pentose sugars and the resultant .............................................................................................................................. 46 Figure 2.1. DNA anti-parallelhelix and a magnified region of the primary structure of DNA showing deoxyribose, phosphate and a nucleic base. ......................................................... 53 Figure 2.2. Product and reagent hydrazone standards. ...................................................... 56 Figure 2.3. ESI mass spectrum for the 2-deoxyribose-forming reaction after 72 hours of trapping. The correct mass of trapped 2-deoxyribose 132 is present. ................................ 66 Figure 2.4. Trapped hydrazone standards and their yields using N,N-diphenyl hydrazine 144 after stirring for 1 hour in methanol and catalytic acetic acid. The crystal structure of 146 is also shown as 50 % ellipsoid. ............................................................................................. 69 Figure 2.5. 500 MHz 1H NMR spectrum of a mixture of hydrazones D-146 and D-147 in methanol d4. ........................................................................................................................ 70 Figure 2.6. 500 MHz 1H NMR spectrum of 2-deoxy-D-ribose hydrazone D-146 in methanol d4. ....................................................................................................................................... 71 Figure 2.7. 500 MHz 1H NMR spectrum of