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

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60 APPENDIX A. PARAMETERS matrix obviously correspond to the type of the AO. The position in the list corresponds to the type of the overlap, where S[0] is a σ-overlap, S[1] is a π-, a hyperconjugation-, or an indirect overlap, and S[2] is a semi-direct or a fictitious overlap (see sect. 3.2). Table A.2: Parameters for the graph orbital model. The top line gives the Coulomb integrals I for the atom orbitals that are currently implemented. Overlap integrals are listed separately for σ and π bonds. Semi-direct and indirect overlaps and banana-bonds in constrained rings are parametrized as the product of the bonding interaction with a scaling factor (see tab. 3.2). σ H C N O s sp 3 sp 2 sp sp 3 sp 2 sp sp 3 sp 2 I -13.6 -13.9 -14.5 -15.4 -16.6 -17.6 -19.7 -19.2 -20.6 H s 0.75 0.69 0.65 0.66 0.62 0.63 0.63 0.55 0.57 C sp 3 0.69 0.65 0.67 0.71 0.60 0.63 0.65 0.54 0.57 C sp 2 0.65 0.67 0.77 0.80 0.70 0.73 0.77 0.64 0.68 C sp 0.66 0.71 0.80 0.87 0.77 0.80 0.84 − − N sp 3 0.62 0.60 0.70 0.77 0.58 0.61 0.65 0.63 0.67 N sp 2 0.63 0.63 0.73 0.80 0.61 0.70 0.73 0.63 0.67 N sp 0.63 0.65 0.77 0.84 0.65 0.73 0.82 − − O sp 3 0.55 0.54 0.64 − 0.63 0.63 − − − O sp 2 0.57 0.57 0.68 − 0.67 0.67 − − − π C N O p p p I -11.4 -13.4 -14.8 C 0.38 0.31 0.26 N 0.31 0.31 0.26 O 0.26 0.26 0.26
Appendix B GRW GRW is implemented in Haskell, a lazy functional programming language [111]. Since it is not easy to glue together pieces of code written in functional and imperative programming languages (e.g. C), the engine is designed as client/server application. The client sends a graph to the server, which performs the rewrite step and sends the transformed graph back to the client. The rewrite behavior of the server only depends on the set of rewriting rules which are read from a file at server startup. This program architecture allows us to easily fit the rewrite engine to the needs of a particular task by simply changing the client. The server can be run in two rewriting modes: random rewrite and priority rewrite. In the former mode a rewrite rule is picked at random from the set of potentially applicable rules, while in the latter mode the rule with the highest “priority value” is chosen. The graph rewrite rules are conveniently specified using the Graph Meta Language (GML) [90]. The specification of the Diels Alder reaction is, for example: # Diels Alder rule [ context [ node [ id 1 label "C" ] node [ id 2 label "C" ] node [ id 3 label "C" ] node [ id 4 label "C" ] node [ id 5 label "C" ] node [ id 6 label "C" ] ] left [ edge [ source 1 target 2 label "=" ] 61
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A Toy Model of Chemical Reaction Ne
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i Dank an alle, die zum Gelingen di
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v Zusammenfassung Chemische Reaktio
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viii CONTENTS B GRW 61 C Organic re
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2 CHAPTER 1. INTRODUCTION ▽ △
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4 CHAPTER 1. INTRODUCTION ¡ ¡ ¡
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6 CHAPTER 1. INTRODUCTION and symme
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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 and 58: 5.3. NETWORK PROPERTIES 47 (see ch.
Page 59 and 60: Chapter 6 Computational results Whe
Page 61 and 62: O O O O O O O O O O O O O O O O O O
Page 63 and 64: 6.3. GRAPH-THEORETIC PROPERTIES 53
Page 65 and 66: Chapter 7 Conclusion and Outlook Th
Page 67 and 68: Using the rules of mass action kine
Page 69: Appendix A Parameters The energy ca
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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A Toy Model of Chemical Reaction Networks - TBI - UniversitÃ¤t Wien

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