Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2014 MOLECULAR DYNAMICS SIMULATIONS OF PURE POLYTETRAFLUOROETHYLENE NEAR GLASSY TRANSITION TEMPERATURE FOR DIFFERENT MOLECULAR WEIGHTS Rawan Al-Nsour Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Mechanical Engineering Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/3845 This Dissertation is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. MOLECULAR DYNAMICS SIMULATIONS OF PURE POLY- TETRAFLUOROETHYLENE NEAR GLASSY TRANSITION TEMPERATURE FOR DIFFERENT MOLECULAR WEIGHTS A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Degree at Virginia Commonwealth University by RAWAN AL-NSOUR M.Sc., Industrial Engineering, University of Jordan, Jordan, 2006 B.Sc., Mechanical Engineering, Jordan University of Science and Technology, Jordan, 2002 Director: Hani El-Kaderi, PhD Associate Professor in Department of Chemistry Virginia Commonwealth University Richmond, Virginia December, 2014 1 Acknowledgment I would like first to express my gratitude to my family; my father, my mother, my lovely husband (Basil), my adorable son (Yazan), my siblings, my father and mother in law and all my big family for their continuous and great support. Basil and Yazan, it was long and challenging journey that will not end with success without your patience, love and encouragement. I want also to express my sincere gratefulness to my doctoral committee, Dr. Hani El-kaderi (Chair), Dr. Brian Hinderliter (Co-Chair), Dr. John Hackett (Co-Chair), Dr. Karla Mossi, and Dr. James McLeskey, for their patience and gaudiness. Each, in their own way, contributed to the quality of my dissertation research and the completion of my doctoral work. My sincere thanks also to Dr. Barbara Boyan, Dr. Gary Tepper, Dr. Neel Scarsdale, and Dr. Justin Elenewski. 2 Table of Contents List of Figures ................................................................................................................................. 6 List of Tables ................................................................................................................................ 10 List of Abbreviations .................................................................................................................... 11 Abstract ..................................................................................................................................... 12 1 Introduction ................................................................................................................................ 14 1.1 Motivations..................................................................................................................... 14 1.2 Outline ............................................................................................................................ 16 2 Background ............................................................................................................................ 17 2.1 Introductory Remarks ..................................................................................................... 17 2.2 Physical Nature .............................................................................................................. 18 2.3 Literature Review ........................................................................................................... 19 2.3.1 Experimental Approach .......................................................................................... 20 2.3.2 Computational Chemistry Approach ...................................................................... 22 2.3.3 Molecular Dynamics Simulations Approach .......................................................... 38 2.4 Macroscopic Properties .................................................................................................. 43 2.4.1 Mechanical Properties ............................................................................................. 44 2.4.2 Thermal Properties .................................................................................................. 46 3 Approach ............................................................................................................................... 50 3.1 Definition ....................................................................................................................... 50 3.2 Why Molecular Dynamics? ............................................................................................ 50 3.3 History ............................................................................................................................ 50 3.4 Molecular Dynamics Basics ........................................................................................... 52 3.4.1 Molecular Mechanics .............................................................................................. 52 3.4.2 Classical Mechanics ................................................................................................ 54 3.4.3 Statistical Mechanics .............................................................................................. 57 3.4.4 Design Optimization ............................................................................................... 58 3.5 General Algorithms ........................................................................................................ 60 4 Methodology .......................................................................................................................... 61 4.1 Force-Field Parameterization ......................................................................................... 61 4.1.1 Intermolecular Interactions ..................................................................................... 64 3 4.1.2 Intramolecular Interactions ..................................................................................... 65 4.2 NAMD Input Files ......................................................................................................... 69 4.2.1 Protein Data Bank File and Single Chain File ........................................................ 70 4.2.2 Protein Structure File .............................................................................................. 72 4.2.3 Parameter File ......................................................................................................... 73 4.2.4 Configuration File ................................................................................................... 73 4.3 Polymer Configuration ................................................................................................... 73 4.4 New Residue Test........................................................................................................... 74 4.5 Amorphous Structure ..................................................................................................... 79 4.6 Computing Glassy Transition Temperature ................................................................... 82 4.7 Measuring Properties Affected by Glassy Transition Temperature ............................... 87 4.7.1 Volumetric Coefficient of Thermal Expansion ....................................................... 87 4.7.2 Specific Volume...................................................................................................... 91 4.7.3 Bulk Modulus.......................................................................................................... 92 4.8 Glassy Transition Temperature Governing Forces at Molecular Level ......................... 94 5 Discussion & Results ............................................................................................................. 97 5.1 The Force-Field Parameters ........................................................................................... 97 5.1.1 B3LYP Derived Parameters .................................................................................... 98 5.1.2 MP2 Derived Parameters ...................................................................................... 107 5.2 Glassy Transition Temperature Analysis ..................................................................... 113 6 Different PTFE Molecular Weight Cells Analysis .............................................................. 117 6.1 PTFE Cells ................................................................................................................... 117 6.2 Amorphous Phase ......................................................................................................... 120 6.2.1 C5F12 Melt Phase ................................................................................................... 120 6.2.2 C8F18 Melt Phase ................................................................................................... 123 6.2.3 C11F24 Melt Phase .................................................................................................. 126 6.2.4 Phase Assessment ................................................................................................. 129 6.3 Melt Phase Analysis ..................................................................................................... 133 6.3.1 Boiling