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Computational Studies on Host-Guest Catalysis

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Computational Studies on Host-Guest Catalysis COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art. 32 del Texto Refundido de la Ley de Propiedad Intelectual (RDL 1/1996). Para otros usos se requiere la autorización previa y expresa de la persona autora. En cualquier caso, en la utilización de sus contenidos se deberá indicar de forma clara el nombre y apellidos de la persona autora y el título de la tesis doctoral. No se autoriza su reproducción u otras formas de explotación efectuadas con fines lucrativos ni su comunicación pública desde un sitio ajeno al servicio TDR. Tampoco se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR (framing). Esta reserva de derechos afecta tanto al contenido de la tesis como a sus resúmenes e índices. WARNING. Access to the contents of this doctoral thesis and its use must respect the rights of the author. It can be used for reference or private study, as well as research and learning activities or materials in the terms established by the 32nd article of the Spanish Consolidated Copyright Act (RDL 1/1996). Express and previous authorization of the author is required for any other uses. In any case, when using its content, full name of the author and title of the thesis must be clearly indicated. Reproduction or other forms of for profit use or public communication from outside TDX service is not allowed. Presentation of its content in a window or frame external to TDX (framing) is not authorized either. These rights affect both the content of the thesis and its abstracts and indexes. UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 Computational studies on host-guest catalysis Charles GOEHRY Doctoral Thesis Institute of Chemical Research of Catalonia (ICIQ) Rovira i Virgili University Tarragona, May 2014 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 Computational studies on host-guest catalysis Doctoral thesis Charles GOEHRY Supervised by Prof. Feliu Maseras Institute of Chemical Research of Catalonia (ICIQ) Rovira i Virgili University Tarragona May 2014 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 ICIQ - Institut Catal`ad’Investigaci´oQu´ımica Avgda. Pa¨ısosCatalans 16, 43007 Tarragona (Spain) WE STATE that the present study, entitled \Computational studies on host-guest catalysis\, presented by Charles GOEHRY for the award of the degree of Doctor, has been carried out under our supervision at the Institute of Chemical Research of Catalonia ICIQ, and that it fulfills all the requirements to be eligible for the European Doctorate Award. Tarragona, 21 May 2014 Doctoral thesis supervisor Doctoral thesis co-supervisor Prof. Dr. Feliu Maseras Dr. Maria Besora UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 Acknowledgements This work has been carried out in the Institute of Chemical Research of Catalonia (ICIQ) in Tarragona (September 2010 - June 2014) under the supervision of Prof. Feliu Maseras and Dr. Maria Besora. I express my warmest thanks to Prof. Feliu Maseras who pro- vided me the opportunity to me come in Tarragona to undertake this thesis. He gave me a lot of freedom and was always support- ive. Without his supervision and constant help this dissertation would not have been possible. I would like thank Dr. Maria Besora for the many things she taught me and her patient help throughout my PhD. I want to thank Prof. Nuria Lopez and Prof. Carles Bo for their kindness, for welcoming students from all over the world, and for taking part in organizing the life of the research center. I would like to thank Dr. Jochen Blumberger for his hospi- tality in his group in UCL (University College London) during the summer of 2012. This was a very important experience to me. I could use new computational tools and to explore a new research field. Special thanks go to Nuria Vendrell. She makes a remarkable job and smoothens all the administrative processes. I received uncountable direct and indirect support from her. I also want to salute my numerous coworkers and former coworkers for the good times spent together and what we learned UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 from each other. Finally my most important acknowledgments are towards my immediate family who have been the single biggest motivating force in my life. I thank my mother Mrs Michele Goehry and my father Dr. Christian Goehry for their encouragement, advice and for the many sacrifices they have made over a number of years. I also thank my sister Miss Pauline Goehry for her support, advice and the joy she brings around herself. Last but not least, I also want to thank my wife Mrs Hanqing Li Goehry. There are uncountable reasons why I should thank her, but there is not enough space for that here. Moreover, I welcome our baby girl Lætitia Goehry, whose birth brought a whole new light in our lives. This dissertation is dedicated to them. UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 Contents 1 Introduction 1 1.1 Supramolecular Chemistry . 1 1.1.1 The Origins of Supramolecular Chemistry 1 1.1.2 Covalent Structures . 2 1.1.3 Self-Assembly . 3 1.1.4 Self-assembled Molecular Flasks . 3 1.2 Non-covalent Interactions . 4 1.2.1 Electrostatics . 5 1.2.2 Dispersion . 5 1.2.3 π − π-Stacking . 6 1.2.4 Hydrogen Bonds . 7 1.2.5 Reversible Metal Bonds . 8 1.3 Catalysis With Supramolecular Systems . 8 1.3.1 Successful Examples of Host-Guest Catal- ysis . 9 1.4 Click Reactions . 15 1.4.1 Organic 1,3-dipolar Cycloaddition . 15 1.4.2 Huisgen 1,3-dipolar Cycloaddition Cat- alyzed by Copper . 16 1.5 Effective molarities . 16 1.6 Computation Studies on Host-Guest Catalysis . 17 1.6.1 Cucurbit[n]uril in Diels-Alder Catalysis . 17 1.6.2 Cucurbit[6]uril Promoting a Click Reaction 17 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 1.6.3 Self-Assembled Capsule Promoting a Diels- Alder Reaction . 18 1.6.4 Enhanced Reactivity of a Triazole For- mation by a Molecular Flask . 18 1.6.5 Acceleration of the Hydrolysis of Ortho- formates by a Self-Assembled Supramolec- ular Cage . 19 2 Computational Methods and Models 23 2.1 Methods . 23 2.1.1 Molecular Mechanics . 23 2.1.2 Hartree-Fock Theory . 26 2.1.3 Basis Functions . 28 2.1.4 Semi-empirical Methods . 30 2.1.5 Density Functional Theory . 30 2.1.6 ONIOM Partition Scheme . 33 2.1.7 Solvation . 34 2.2 Applicability to Supramolecular Systems and Limits 35 2.3 Methods Used in This Study . 36 2.3.1 Solvent Effects . 37 2.3.2 Basis Set Superposition Error . 37 2.3.3 Standard States . 38 2.3.4 Geometry Optimization . 38 2.4 Kinetic Model . 40 3 Cucurbituril 45 3.1 The Host . 45 3.2 An Efficient Host for a Cycloaddition . 46 3.2.1 The Turnover Issue . 47 3.2.2 Identifying a Suitable Theoretical Method 47 3.3 Results . 47 3.3.1 Reactive Molecules Captured . 47 UNIVERSITAT ROVIRA I VIRGILI COMPUTATIONAL STUDIES ON HOST-GUEST CATALYSIS. Charles Goehry Dipòsit Legal: T 1545-2014 3.3.2 Reaction Inside the Macrocycle . 51 3.3.3 Product Release . 51 3.3.4 Basis Set Superposition Error .
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