University of Groningen
Self-replicators from dynamic molecular networks: selection, competition and subsystem
coupling
Komáromy, Dávid
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Komáromy, D. (2019). Self-replicators from dynamic molecular networks: selection, competition and subsystem coupling. University of Groningen.
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Self-Replicators from Dynamic Molecular
Networks: Selection, Competition and
Subsystem Coupling
The work described in this thesis was carried out in the Stratingh Institute
for Chemistry, University of Groningen, The Netherlands.
This work was financially supported by the European Union through the
COST Action CM1304 (“Emergence and Evolution of Complex Chemical
Systems)” and the University of Groningen).
Printed by Gildeprint, Enschede, The Netherlands.
Self-Replicators from Dynamic Molecular
Networks: Selection, Competition and
Subsystem Coupling
Proefschrift
ter verkrijging van de graad van doctor aan
de Rijksuniversiteit Groningen
op gezag van de
Rector Magnificus prof dr. E. Sterken
en volgens besluit van het College voor Promoties.
De openbare verdediging zal plaatsvinden op
Vrijdag 8 maart 2019 om 16.15 uur
door
Dávid Komáromy
geboren op 7 januari 1985
Promotores
Prof. dr. S. Otto
Prof. dr. S. R. Harutyunyan
Beordelingscomissie
Prof. dr. R. C. Chiechi
Prof. dr. W. Huck
Prof. dr. N. Giuseppone
Table of Contents
Chapter 1 ... 9
1.1. Introduction ... 10
1.2. Reaction Networks: Dynamic Combinatorial Libraries ... 10
1.2.1. Dynamic Combinatorial Chemistry ... 10
1.2.2. Dynamic Combinatorial Libraries ... 12
1.3. Self-Assembly ... 20
1.3.1. General Features of Chemical Self-Assembly ... 20
1.3.2. Subcomponent Self-Assembly ... 23
1.3.3. Self-Sorting ... 25
1.3.4. Self- and Cross-Replication ... 26
1.3.5. Self-Organization ... 32
1.4. Subsystem Coupling ... 34
1.5. Content of this Thesis ... 38
1.6. Acknowledgements ... 39
1.7. References ... 39
Chapter 2 ... 43
2.1. Introduction ... 44
2.2. Results and Discussion ... 45
2.3. Conclusions ... 57
2.4. Supporting Information ... 59
2.4.1. General remarks ... 59
2.4.2. Synthetic Procedures ... 60
2.4.3. NMR Spectra ... 63
2.4.4. UPLC chromatograms of monomers 1, 2, and 3. ... 72
2.4.5. Procedure for preparation of DCLs with perborate-mediated oxidation ... 72
2.4.6. LC-MS analyses of DCLs ... 73
2.4.7. General remark on the topology of LMCs based on the mass spectra ... 73
2.4.8. Additional data on the LMCs from building block 1 ... 74
2.4.9. Additional characterization of the LMCs formed from building block 2. ... 75
2.4.11. Additional characterization of hexamer 16 ... 77
2.4.12. Additional characterization of tetramer 24 ... 81
2.5. Author Contributions ... 82
2.6. References ... 82
Chapter 3 ... 85
3.1. Introduction ... 86
3.2. Results and Discussion ... 87
3.3. Conclusions ... 95 3.4. Supporting Information ... 96 3.4.2. General Procedures ... 96 3.4.3. LC-MS analyses of DCLs ... 97 3.4.4. Control Experiments ... 98 3.4.5. Additional Experiments ... 101 3.5. Author Contributions ... 102 3.6. References ... 103 Chapter 4 ... 105 4.1. Introduction ... 106
4.2. Results and discussion ... 108
4.2.1. Investigation of the (1+2)-system ... 108
4.2.2. Investigation of the (1+3)-system ... 122
4.3. Conclusion ... 129 4.4. Supporting Information ... 132 4.4.1. General remarks ... 132 4.4.2. Library preparation ... 134 4.4.3. Seeding experiments ... 134 4.4.4. LC-MS analyses of DCLs ... 136 4.4.5. Supporting experiments ... 154 4.5. Author Contributions ... 158 4.6. References ... 158 Chapter 5 ... 161 5.1. Introduction ... 162
5.2. Results and Discussion ... 165
5.2.2. Structure and assembly of the mixed hexamer 1442 ... 167
5.2.3. Structure and assembly of the mixed tetramer 1143... 175
5.2.4. Relative stabilities of the self-assembling species in the (1+4)-system ... 182
5.2.5. Substrate scope ... 185
5.3. Conclusions ... 187
5.4. Supporting Information ... 189
5.4.1. General remarks ... 189
5.4.2. Synthesis of building block 6 ... 192
5.4.3. LC-MS analyses of DCLs ... 194
5.4.4. Detailed stoichiometric study of DCLs composed of 1 and 4 ... 213
5.4.5. Tandem mass spectroscopy of 1442 ... 214
5.4.6. Analysis of the assemblies of 18 and 1442 with spectroscopy and TEM ... 215
5.4.7. Kinetic analyses of the formation of 1442 ... 218
5.4.8. UPLC and TEM analyses of the formation of 1143 ... 220
5.4.9. Full 1H-NMR assignment of 1 ... 221
5.4.10. Full 1H-NMR assignment of 1143. ... 224
5.4.11. Direct injection Orbitrap analysis of 1143 ... 230
5.4.12. Mutual interconversion experiments in the 1+4 system. ... 230
5.4.13. Structural characterization of the peptide analogues of 1143 and 1244 .... 232
5.5. Author Contributions ... 233
5.6. References ... 233
Chapter 6 ... 235
6.1. Summary ... 236
6.2. Conclusions and Outlook ... 239
6.2.1. Conclusions... 239
6.2.2. Outlook ... 240
6.2.3. Systems Chemistry and the Current Culture of Science ... 242
6.3. References ... 242
Samenvatting ... 236
