A Toy Model of Chemical Reaction Networks - TBI - UniversitÃ¤t Wien

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48 CHAPTER 5. REACTION NETWORKS
Chapter 6 Computational results When the three components molecules, reactions, and network simulation are put together, it is possible to build a CRN performing molecular property prediction and model reduction on the fly, given only a list of initial SMILES. For the following CRNs, regioselectivity was simulated using the simple equations described at the end of section 3.6. 6.1 Repetitive Diels-Alder reactions The Diels-Alder reaction [25] has been extensively studied thanks to its importance in natural products synthesis and because it is easily tractable by simple semi-empirical methods. It is the typical test reaction for a semiempirical quantum calculation methods such as ours, and furthermore for the numerous approaches of reaction description [110]. It involves the reaction between two linear π-systems of length 2 and 4, called dienophiles and dienes, and is thus called a [2+4]-cycloaddition. The product is again a dienophile and may react again in a Diels-Alder reaction, then termed repetitive. Indeed, the reaction is used for the synthesis of polymers [80]. The CRN in fig. 6.1 is obtained by repetitive Diels-Alder reactions of a simple initial mixture of dienes and dienophiles. The rewrite rule is a bimolecular variant of the one described in fig. 4.2 (see appendix B). The simple constraints derived from FMO lead to a reaction respecting the Woodward-Hoffmann rules [126]. Depending on which choice makes |∆E FMO | smaller, the HOMO of the diene or dienophile reacts with the LUMO of the complementary species. The orientation of the reactants to each other is determined by the FMO coefficients. Model reduction consisted in producing only one of regioisomers instead of both. A further reduction was introduced by an enthalpy threshold of 20 eV. 49
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A Toy Model of Chemical Reaction Ne
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i Dank an alle, die zum Gelingen di
Page 7: v Zusammenfassung Chemische Reaktio
Page 10 and 11: viii CONTENTS B GRW 61 C Organic re
Page 12 and 13: 2 CHAPTER 1. INTRODUCTION ▽ △
Page 14 and 15: 4 CHAPTER 1. INTRODUCTION ¡ ¡ ¡
Page 16 and 17: 6 CHAPTER 1. INTRODUCTION and symme
Page 18 and 19: 8 CHAPTER 2. ARTIFICIAL CHEMISTRIES
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Page 25 and 26: 3.1. EXTENDED HÜCKEL THEORY 15 is
Page 27 and 28: 3.2. FURTHER APPROXIMATIONS 17 K. F
Page 29 and 30: 3.2. FURTHER APPROXIMATIONS 19 Figu
Page 31 and 32: 3.2. FURTHER APPROXIMATIONS 21 are
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Page 37 and 38: 3.4. WAVE FUNCTION ANALYSIS 27 Derw
Page 39 and 40: Table 3.6: Overlap matrix for prope
Page 41 and 42: 3.5. PERFORMANCE 31 3.5 Performance
Page 43 and 44: 3.6. FRONTIER MOLECULAR ORBITAL THE
Page 45 and 46: Chapter 4 Chemical reactions A mole
Page 47 and 48: 4.1. GRAPH REWRITING 37 Graphical t
Page 49 and 50: 4.1. GRAPH REWRITING 39 C C C C C C
Page 51 and 52: 4.2. GRAPH REWRITE ENGINE 41 O O O
Page 53 and 54: Chapter 5 Reaction networks 5.1 Net
Page 55 and 56: 5.3. NETWORK PROPERTIES 45 O 3 NO 3
Page 57: 5.3. NETWORK PROPERTIES 47 (see ch.
Page 61 and 62: O O O O O O O O O O O O O O O O O O
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Page 65 and 66: Chapter 7 Conclusion and Outlook Th
Page 67 and 68: Using the rules of mass action kine
Page 69 and 70: Appendix A Parameters The energy ca
Page 71 and 72: Appendix B GRW GRW is implemented i
Page 73 and 74: Appendix C Organic reactions Fromht
Page 75 and 76: Bibliography [1] R. Albert and A.-L
Page 77 and 78: BIBLIOGRAPHY 67 [25] O. Diels and K
Page 79 and 80: BIBLIOGRAPHY 69 [50] J. Gasteiger a
Page 81 and 82: BIBLIOGRAPHY 71 [76] W. Langenbeck.
Page 83 and 84: BIBLIOGRAPHY 73 [102] S. Schuster,
Page 85: BIBLIOGRAPHY 75 [126] R. Woodward a
Page 89 and 90: The Wooing of Archibald Modern tren
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