University of Groningen Controlling the motion of molecular machines at the nanoscale Ruangsupapichat, Nopporn IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2012 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Ruangsupapichat, N. (2012). Controlling the motion of molecular machines at the nanoscale. s.n. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 09-10-2021 Controlling the Motion of Molecular Machines at the Nanoscale Nopporn Ruangsupapichat The work described in this thesis was carried out at the Stratingh Institute for Chemistry, University of Groningen, The Netherlands. This work was financially supported by the Zernike Institute for Advanced Materials. Printed by: Ipskamp Drukkers B. V., Enschede, The Netherlands. Cover designed and made by: Martin Roelfs and Randy Wind RIJKSUNIVERSITEIT GRONINGEN Controlling the Motion of Molecular Machines at the Nanoscale Proefschrift ter verkrijging van het doctoraat in de Wiskunde en Natuurwetenschappen aan de Rijksuniversiteit Groningen op gezag van de Rector Magnificus, dr. E. Sterken, in het openbaar te verdedigen op vrijdag 27 april 2012 om 14:30 uur door Nopporn Ruangsupapichat geboren op 2 februari 1981 te Rayong, Thailand Promotor: Prof. dr. B. L. Feringa Copromotor: Dr. S. R. Harutyunyan Beoordelingscommissie: Prof. dr. R. J. M. Nolte Prof. dr. ir. A. J. Minnaard Prof. dr. A. Herrmann ISBN (printed version): 978-90-367-5373-9 ISBN (digital version): 978-90-367-5372-2 Contents Chapter 1 From the Machinery of Life to Artificial Molecular Machines 1 1.1 Introduction 2 1.2 Molecular machines in living cells 3 1.3 Artificial molecular machines 7 1.3.1 Molecular rotors 7 1.3.1.1 Molecular shuttle rotaxanes and catenanes 7 1.3.1.2 Molecular switches: stilbenes, overcrowded alkenes and azobenzens 14 1.3.1.3 Molecular propellers, gears and breaks 19 1.3.2 Molecular motors 22 1.3.2.1 Chemically-driven molecular motors 22 1.3.2.2 Photochemiclly-driven molecular motors 24 1.4 Towards applications of molecular machines at the nanoscale 30 1.4.1 Works performed by functional molecular machines 30 1.4.2 Single-molecular-sized machines moving on surfaces 33 1.5 Aims of the research and outline of this thesis 36 1.6 References 38 Chapter 2 New Design of Molecular Motors: Toward Functional Motors 45 2.1 Introduction 46 2.1.1 Rate of rotation by structural modifications of first-generation molecular motors 46 2.1.2 Rate of rotation depending on different structural modifications of second- generation molecular motors 50 2.2 Results and Discussions 54 2.2.1 Short synthetic route to prepare the upper-half of a functionalized molecular motor 54 2.2.2 Design and synthesis of the motor-porphyrin hybrid 59 2.2.3 Synthesis of D-aryl substituent ketones for the molecular hybrid-motors 63 2.2.4 New functionalized first-generation molecular motor 68 2.3 Conclusions 74 2.4 Acknowledgements 75 2.5 Experimental Section 75 General remarks 75 Synthesis of all compounds 75 2.6 References 85 Chapter 3 Toward Oscillating Biaryl-Allyl Ester and Derivatives Driven by Catalysis (Molecular Oscillator) 89 3.1 Introduction 90 3.2 Results and Discussions 98 3.2.1 Molecular design 98 3.2.2 The synthesis of biaryl-allyl ester 3 100 3.2.3 The palladium-complex of compound 3 101 3.2.4 The palladium-catalyzed allylic substitution properties of compound 3 102 3.2.5 The palladium-catalyzed rearrangements involving the C1-O ĺ C3-O conversion 103 3.2.6 The synthesis of 7,12-diphenyl-biaryl-allyl ester 14 107 3.2.7 The Pd-catalyzed rearrangements involving the C1-OĺC3-O conversion of compound 14 108 3.2.8 DFT calculations 109 3.3 Conclusions 113 3.4 Acknowledgements 114 3.5 Experimental Section 114 X-ray crystallographic data of compound 9 114 Synthesis of all compounds 115 3.6 References 124 Chapter 4 Reversing the Direction in Light-Driven Rotary Molecular Motors 127 4.1 Introduction 128 4.2 Results and Discussions 131 4.2.1 Molecular design 131 4.2.2 The synthesis of reversible molecular motor 3 135 4.2.3 Spectroscopic measurements of photochemical, thermal and base-catalyzed isomerizations of molecular motor 3 135 4.2.4 The synthesis of reversible molecular motor 4 138 4.2.5 Photochemical and thermal-induced isomerizations of motor 4 139 4.2.6 Base-catalyzed epimerization of a reversible molecular motor 4 143 4.2.7 Controlling the rotary process: photochemical, thermal, and base-catalyzed isomerization of a reversible molecular motor 4 144 4.3 Conclusions 148 4.4 Experimental section 148 General procedure for isomerization processes 148 Synthesis of all compounds 149 4.5 References 154 Chapter 5 From Molecular Motors to Autonomous Movement of Molecular Nanocars 157 5.1 Introduction 158 5.1.1 Molecular design 163 5.1.2 Directional movement depends on the chirality of the structure 164 5.2 Results and Discussions 166 5.2.1 9-Ethynyl-9H-carbazole-based molecular chassis with alkoxy chains 166 5.2.2 9-Ethynyl-9H-carbazole-based molecular chassis with alkyl chains 170 5.2.3 9-Phenyl-9H-carbazole-based molecular chassis 173 5.2.4 Photochemical and thermal isomerization studies of molecular nanocar and related compounds 175 5.3 Conclusions 185 5.4 Acknowledgements 186 5.5 Experimental Section (synthesis of all compounds) 186 5.6 References 196 Chapter 6 From Molecular Motors to Translational Movement of the 2nd Design Molecular Nanocar 199 6.1 Introduction 200 6.2 Results and Discussions 202 6.2.1 Molecular design 202 6.2.2 Synthesis of molecular nanocar 208 6.2.3 Additional synthesis of mono-motor for nanocar comparison 216 6.2.4 Photochemical and thermal isomerization studies 218 6.2.5 Single molecular spectroscopy on molecular nanocar 225 6.3 Conclusions 232 6.4 Acknowledgements 233 6.5 Experimental section 233 General remarks 233 X-ray crystallographic data of compound 8 233 Synthesis of all compounds 235 6.6 References 246 Samenvatting 249 Summary 253 Acknowledgements 257 Chapter 1 From the Machinery of Life to Artificial Molecular Machines An overview of the literature studies, covering development of several types of artificial molecular machines, which were inspired by nature and are of potential use in the nanotechnology field, was described. The main part concerned the construction of artificial molecular machines (molecular rotors and molecular motors) in solution systems. The final part of this chapter provided a short overview regarding the applications of artificial molecular systems, and their high potential towards the development of advanced molecular machinery using nanoscale motion. Chapter 1 1.1 Introduction The molecules that life is built upon, both whole organisms and cells, still mysterify, despite the advances made in molecular science over the last century. For scientists, it is difficult to visualize and comprehend how nature’s molecular machines work. These tiny machines are fundamentally different to those in the macroscopic world of everyday life. Not simply by the billion-fold difference in size but also by the fact that the molecules in living cells perform their job in a world alien to us and hence we must be cautious in our attempts to understand and rationalize the processes behind directed molecular motion. The Newtonian physics and mechanics that allows us to understand the motion of objects in everyday life (gravity, friction and temperature) fails at the molecular nano-scale. Individual molecules are chaperoned, sorted, and shuffled from one place to another, and are used to build entirely new molecules. It is nanoscale molecular machines, such as ATP synthase,1 that are responsible for life’s nanoscale processes. As with the machines of our macroscopic world, these machines perform specific tasks efficiently and precisely. These tasks need to be performed with molecular-sized objects and the molecular machines in cells have been optimized to work at the atomic level. Of particular interest are the biomolecular motors that are equipped with catalytic systems that can convert chemical energy to produce stepwise linear or rotary motion.2 In the last few decades, scientists attempted to manipulate these complex biological machines outside the cell to perform work. Designing and building new and powerful artificial nanoscale motors and propulsion systems are one of the major challenges. Recent research to address these challenges has been covered in several reviews.3 In addition to the motility of artificial machines, another challenge is to keep the machines going in a controlled direction in order to navigate them towards their target or allow them to perform certain functions.