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Model-Driven Engineering in Supramolecular Systems Model-driven engineering in supramolecular systems Citation for published version (APA): Paffen, T. F. E. (2017). Model-driven engineering in supramolecular systems. Technische Universiteit Eindhoven. Document status and date: Published: 15/11/2017 Document Version: Publisher’s PDF, also known as Version of Record (includes final page, issue and volume numbers) Please check the document version of this publication: • A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal. If the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license above, please follow below link for the End User Agreement: www.tue.nl/taverne Take down policy If you believe that this document breaches copyright please contact us at: [email protected] providing details and we will investigate your claim. Download date: 06. Oct. 2021 Model‐driven engineering in supramolecular systems PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Technische Universiteit Eindhoven, op gezag van de rector magnificus prof.dr.ir. F.P.T. Baaijens, voor een commissie aangewezen door het College voor Promoties, in het openbaar te verdedigen op woensdag 15 november 2017 om 16:00 uur door Tim Fransiscus Elizabeth Paffen geboren te Kerkrade Dit proefschrift is goedgekeurd door de promotoren en de samenstelling van de promotiecommissie is als volgt: voorzitter: prof.dr.ir. E.J.M Hensen promotor: prof.dr. E.W. Meijer copromotor: dr.ir. T.F.A. de Greef leden: prof.dr. J.S. Moore (University of Illinois) prof.dr.ir. J. Huskens (Universiteit Twente) dr. G.M. Pavan (University of Applied Sciences and Arts of Southern Switzerland) dr.ir. P.A. Korevaar (Radboud Universiteit Nijmegen) dr.ir. A.R.A. Palmans Het onderzoek of ontwerp dat in dit proefschrift wordt beschreven is uitgevoerd in overeenstemming met de TU/e Gedragscode Wetenschapsbeoefening. Cover design: Tim Paffen Printed by: Gildeprint – the Netherlands A catalogue record is available from the Eindhoven University of Technology Library ISBN: 978‐90‐386‐4375‐5 This work has been financially supported by the Netherlands Organization for Scientific Research (NWO) Table of Contents Chapter 1 Increasing complexity of supramolecular systems .................................................... 1 1.1 Introduction ............................................................................................................... 2 1.2 Molecular competition .............................................................................................. 3 1.3 Multivalency and cooperativity ................................................................................. 4 1.4 Ring‐chain equilibria of divalent molecules ............................................................... 7 1.5 Supramolecular binding motifs: UPy‐NaPy dimerization........................................... 9 1.6 Aim and outline ......................................................................................................... 10 1.7 References ................................................................................................................. 11 Chapter 2 Mathematical modeling of supramolecular systems ................................................. 17 2.1 Introduction ............................................................................................................... 18 2.2 Thermodynamic equilibrium: mass balances ............................................................ 18 2.3 Deterministic kinetic simulations .............................................................................. 22 2.4 Rule‐based modeling ................................................................................................. 25 2.5 Non‐linear regression of experimental data .............................................................. 27 2.6 Decreasing computational time ................................................................................. 30 2.7 Conclusion ................................................................................................................. 30 2.8 Experimental section ................................................................................................. 31 2.9 References ................................................................................................................. 31 Chapter 3 Supramolecular buffering by ring‐chain competition ................................................ 33 3.1 Introduction ............................................................................................................... 34 3.2 Results and discussion ............................................................................................... 35 3.2.1 Model outline ....................................................................................................... 35 3.2.2 Model validation .................................................................................................. 40 3.2.3 Design principles of supramolecular ring‐chain buffering ................................... 43 3.2.4 Buffering via a ring‐chain mechanism versus other buffering mechanisms ........ 45 3.3 Conclusions ................................................................................................................ 47 3.4 Experimental section ................................................................................................. 47 3.4.1 Materials and methods ........................................................................................ 47 3.4.2 Synthetic procedures ........................................................................................... 48 3.4.3 Model description of two‐component supramolecular buffering ....................... 50 3.4.4 Assignment of 1H NMR urethane proton resonances and analysis of ring‐chain equilibrium ........................................................................................................... 56 3.4.5 Influence of oligomeric rings on buffering ........................................................... 60 3.4.6 Calculation of confidence interval on CNaPy free ..................................................... 62 3.4.7 UV‐VIS data of ditopic UPy 3‐NaPy 2 mixtures .................................................... 64 3.5 References ................................................................................................................. 64 Chapter 4 Model‐driven engineering of improved supramolecular buffering by multivalency ... 69 4.1 Introduction ............................................................................................................... 70 4.2 Results ........................................................................................................................ 71 4.3 Discussion .................................................................................................................. 79 4.4 Experimental section ................................................................................................. 80 4.4.1 Model description of tri‐ and tetravalent UPys with NaPy .................................. 80 4.4.2 Determination of KUPy‐UPy, KUPy‐NaPy and EM1 ......................................................... 88 4.4.3 Fit of 1H NMR data of NaPy 5 mixtures with trivalent UPy 3 or tetravalent UPy 4 .................................................................................................................... 89 4.4.4 Model description and fit of the tetravalent UPy 4 and NaPy 5 titration using DPU 6 ................................................................................................................... 92 4.5 References ................................................................................................................. 94 Chapter 5 Regulating competing supramolecular interactions using ligand concentration ........ 97 5.1 Introduction ............................................................................................................... 98 5.2 Results and discussion ............................................................................................... 99 5.2.1 Model outline ....................................................................................................... 99 5.2.2 Non‐linear regression of experimental titration data .......................................... 103 5.3 Conclusion ................................................................................................................
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