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Molecular Transport and Reactivity in Confinement

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Molecular Transport and Reactivity in Confinement Molecular Transport and Reactivity in Confinement THU NGOC LE A dissertation submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy of the University College London Department of Chemical Engineering Primary Advisor: Professor Alberto Striolo December 2016 Declaration I, Thu Ngoc Le confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that they have been properly indicated in the thesis. 1 To my parents Phuong Le and Thu Do Kính tặng bố mẹ vì tình yêu thương vô bờ dành cho con 2 Acknowledgements It is my genuine pleasure to express my deepest thanks and gratitude to my advisor Professor Alberto Striolo, whose expertise, support and guidance have helped me tremendously in completing my PhD study. I would like to extend my sincere gratitude to Professor Heath Turner from University of Alabama for his generosity, kindness and encouragement on the most difficult topic of my study. I would like to give immense appreciation to Dr. Paul Ashby from Lawrence Berkeley National Laboratory and Professor Roy Penny from University of Arkansas for teaching me, not only valuable academic knowledge, but also how to be a better person. Thank you for having much faith in me. This thesis is especially dedicated to my Father and Mother, who have always been my inexorable stronghold. Being brought to the world as your daughter is the upmost divine blessing I could ever ask for in this life. To my sisters Han Le and Tran Le, I am thankful for being my upright idols, my greatest supports, and my best friends. Last of all, I would like to give special thanks to Shane Do, Rami Akkari, Dr. Manaswee Suttipong, Dr. Siddharth Gautam, Dr. Hieu Pham and everyone else who, either directly or indirectly, have kindly lent their helping hands in my challenging yet rewarding venture. 3 Contents List of Abbreviations ............................................................................................................... 7 List of Tables ............................................................................................................................ 8 List of Figures ........................................................................................................................... 9 Abstract ............................................................................................................................ 16 Chapter 1. Introduction ...................................................................................................... 17 Chapter 2. Model and Methodology .................................................................................. 22 2.1. SIMULATION MODEL AND METHODOLOGY ................................................. 22 2.2. MOLECULAR DYNAMICS (MD).......................................................................... 29 2.2.1. Basic Background .............................................................................................. 29 2.2.2. MD Algorithm ................................................................................................... 29 2.2.3. Leap-frog Algorithm .......................................................................................... 30 2.2.4. Periodic Boundary Condition (PBC) and Centre of Mass (COM) Calculation in PBC ............................................................................................................................ 31 2.2.5. Simulation Details .............................................................................................. 32 2.3. REACTIVE ENSEMBLE MONTE CARLO (RXMC) ............................................ 32 2.4. RESULT ANALYSIS ............................................................................................... 34 2.4.1. Mean Square Displacement and Diffusion Coefficient, Ds ............................... 34 2.4.2. Diffusion Activation Energy, Ea ........................................................................ 35 2.4.3. Residence Autocorrelation Function, CR ........................................................... 35 2.4.4. Radial Distribution Functions, g(r) .................................................................... 36 Chapter 3. Confinement of Pure Propane ........................................................................ 38 3.1. ABSTRACT .............................................................................................................. 38 3.2. INTRODUCTION ..................................................................................................... 38 3.3. SIMULATION METHODOLOGY .......................................................................... 40 3.4. RESULTS AND DISCUSSION ............................................................................... 44 3.4.1. Simulated Adsorption Isotherms........................................................................ 45 3.4.2. Molecular Structure of Confined Propane ......................................................... 48 3.4.3. Dynamical Properties for Confined Propane ..................................................... 50 3.5. CONCLUSIONS ....................................................................................................... 53 Chapter 4. Confinement of Long Chain Alkane and Carbon Dioxide Mixtures .......... 54 4.1. ABSTRACT .............................................................................................................. 54 4.2. N-BUTANE AND CO2 ............................................................................................. 54 4 4.2.1. INTRODUCTION ............................................................................................. 54 4.2.2. SIMULATION METHODOLOGY................................................................... 56 4.2.3. RESULTS AND DISCUSSIONS ...................................................................... 58 4.2.4. CONCLUSIONS................................................................................................ 73 4.3. N-OCTANE AND CO2 ............................................................................................. 74 4.3.1. INTRODUCTION ............................................................................................. 74 4.3.2. SIMULATION METHODOLOGY................................................................... 74 4.3.3. RESULTS AND DISCUSSION ........................................................................ 76 4.3.4. CONCLUSIONS................................................................................................ 84 Chapter 5. Confinement Effects on the Hydrogenation of Carbon Dioxide ................. 86 5.1. ABSTRACT .............................................................................................................. 86 5.2. LITERATURE RE-EVALUATION ......................................................................... 86 5.2.1. The Fugacity of Hydrogen Is Set By Mineral Buffer Assemblages .................. 87 5.2.2. Hydrogen-Fugacity at Conditions for Which the CO2 Fugacity Equals That of CH4 ............................................................................................................................ 88 5.3. INTRODUCTION ..................................................................................................... 90 5.4. SIMULATION DETAILS ........................................................................................ 94 5.4.1. Reaction Mechanism .......................................................................................... 94 5.4.2. Specifications for the Sabatier Reaction ............................................................ 96 5.4.3. Molecular Models .............................................................................................. 97 5.4.4. Silica Slit-Shape Pore Models ........................................................................... 97 5.5. RESULTS AND DISCUSSION ............................................................................... 98 5.5.1. Bulk Phase ......................................................................................................... 98 5.5.2. System in the Presence of Confinement .......................................................... 101 5.6. CONCLUSIONS ..................................................................................................... 112 Chapter 6. Summary and Outlook .................................................................................. 114 6.1. SUMMARY ............................................................................................................ 114 6.2. MULTI-REACTIONS REACTIVE ENSEMBLE MONTE CARLO, REACTIVE FORCE FIELD MONTE CARLO AND RXMC IN COMBINATION WITH TRANSITION-STATE THEORY ..................................................................................... 115 Appendix – Quasielastic Incoherent Neutron Scattering and Bridge to Molecular Dynamics Simulation ........................................................................................................... 117 A.1. INTRODUCTION TO NEUTRON SCATTERING .............................................. 117 A.2. SIMULATION DETAILS ...................................................................................... 123 5 A.2.1. Molecular Models ............................................................................................ 123 A.2.2. Silica Models ................................................................................................... 123 A.2.3. Simulation Methodology ................................................................................
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