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Developing Reactive Molecular Dynamics for Understanding Polymer Chemical Kinetics Kenneth D University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 5-2009 Developing Reactive Molecular Dynamics for Understanding Polymer Chemical Kinetics Kenneth D. Smith University of Massachusetts Amherst, [email protected] Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Polymer Science Commons Recommended Citation Smith, Kenneth D., "Developing Reactive Molecular Dynamics for Understanding Polymer Chemical Kinetics" (2009). Open Access Dissertations. 80. https://doi.org/10.7275/9d4y-2g78 https://scholarworks.umass.edu/open_access_dissertations/80 This Open Access Dissertation is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. DEVELOPING REACTIVE MOLECULAR DYNAMICS FOR UNDERSTANDING POLYMER CHEMICAL KINETICS A Dissertation Presented by KENNETH D SMITH Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2009 Chemical Engineering c Copyright by Kenneth D Smith 2009 All Rights Reserved DEVELOPING REACTIVE MOLECULAR DYNAMICS FOR UNDERSTANDING POLYMER CHEMICAL KINETICS A Dissertation Presented by KENNETH D SMITH Approved as to style and content by: Phillip R. Westmoreland, Chair Dimitrios Maroudas, Member Murugappan Muthukumar, Member T. J. Mountziaris, Department Head Chemical Engineering ACKNOWLEDGMENTS While at UMASS there have been many challenges, but after all that is what a dissertation is all about. While the challenges of fire safe polymers, reactive molecular dynamics, and everything else are not yet resolved, the challenge of finishing the dissertation is completed. I would first like to thank my advisor, Phil Westmoreland. Phil provided a lot of valuable insight and knowledge, and his guidance and support were absolutely necessary for completing this dissertation. He took time to help guide me through many different aspects of life as a graduate student, and I am grateful for all that he has provided. I would also like to thank Prof. Maroudas and Prof. Muthukumar for their participating in my dissertation committee and guidance. Marc Nyden and Stas Stoliarov were also instrumental in the work of this disserta- tion. They took time to help argue and work through many issues that arose through the course of this dissertation. It was also an enjoyable time spent working together on the code at the FAA, where many great discussions help to form the course of this work. This work was also possible only through the funding of the Center for UMASS- Industry Research on Polymers (CUMIRP) Cluster F for Fire-Safe Polymers, who sponsored my work for five years. Currently, the cluster is made up of Boeing, Federal Aviation Administration, Multina, NIST, Sekisui Chemical, Solvay, and US Army; although, there have been other supporters as well in the past that I cannot remember at the moment. I would also like to acknowledge the time granted by the National Center for Supercomputing Applications for use of the supercomputers for some of the computational work completed in this dissertation. iv The environment and support of the university and specifically the Chemical En- gineering Department has made the time quite enjoyable. I would like to thank all the staff and faculty for their time and support in many activities from classes to what seem to be minor details. It was always a great group of individuals who made everything go as smoothly as possible. Additionally, there have been many friends throughout the area who have helped me through my times in school. Several at school who provided help, and much needed breaks when everything seemed overwhelming. Also friends from church who have been immensely supportive through everything and kept me sane and on the right path. And also friends from work who consistently encouraged me to finish up. My family has been very supportive and loving through all the endeavors of grad- uate school. Although they may not understand chemical engineering, there love and support has made this possible. I would like to thank my parents, sister, and grandparents for all the encouragement they have provided during the course of my studies. I also must thank my wife, Amy, for all her loving support through many long and tough times during my dissertation. Her support through it has meant a lot to me and has helped me to be able to finish this dissertation. I love you. Finally, I must thank God for granting me the abilities and patience accomplish this task. It was truly not something I could have ever done myself. v ABSTRACT DEVELOPING REACTIVE MOLECULAR DYNAMICS FOR UNDERSTANDING POLYMER CHEMICAL KINETICS MAY 2009 KENNETH D SMITH B.S., ROWAN UNIVERSITY M.ChE., UNIVERSITY OF DELAWARE Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Phillip R. Westmoreland One of the challenges in understanding polymer flammability is the lack of infor- mation about microscopic events that lead to macroscopically observed species, and Reactive Molecular Dynamics is a promising approach to obtain this crucially needed information. The development of a predictive method for condensed-phase reaction kinetics can provide significant insight into polymer flammability, thus helping guide future synthesis of fire-resistant polymers. Through this dissertation, a new reactive forcefield, RMDff, and Reactive Molecular Dynamics program, RxnMD, have been developed and used to simulate such material chemistry. It is necessary to have accurate description of chemical kinetics to describe quanti- tative chemical kinetics. Typical equilibrium forcefields are inadequate for describing chemical reactions due to the inability to represent bonding transformations. This vi issue was resolved by developing a new method, RMDff, that allows standard equilib- rium forcefields to describe reactive transitions. The chemical reactions are described by employing switching functions that permit smooth transitions between the reac- tant and product descriptions available from traditional forcefields. Because all of the chemical motions are described, a complete potential energy surface is obtained for the course of the reaction. Descriptions of scission, addition/beta-scission, and ab- straction reactions were developed for hydrocarbon species. Reactive potentials were developed using a representative reaction involving small molecules. It is shown that the overall geometric and energetic changes are transferable to larger and substituted molecules. The main source of error found in RMDff resulted from errors within the equilibrium forcefield descriptions. In order to simulate the chemical kinetics, it was necessary to create a molecular dynamics program that could implement the reactions from RMDff. RxnMD was developed as a new C++-based Reactive Molecular Dynamics code to simulate the dynamics using RMDff. Polymer kinetics were predicted for high-density polyethy- lene and used to test the method and code. Conformational changes and polymer length in the initial polyethylene molecules did not significantly alter the backbone decomposition kinetics. The results also revealed that the backbone carbon-carbon bonds could break with an activation energy approximately 100 kJ/mol below the carbon-carbon bond dissociation energy. This decrease was believed to occur from intramolecular polymer stress, which is relieved via backbone scission. Such stress was also observed to increase the beta-scission reaction rate at high temperatures, apparently because the scission reaction alone is not always sufficient to remove the energy associated with the polymer stress concentrated near the scission location. Fi- nally, the RMD method was also shown to be transferable and applicable in describing the decomposition of novel fire-resistant polymers. vii TABLE OF CONTENTS Page ACKNOWLEDGMENTS ............................................. iv ABSTRACT .......................................................... vi LIST OF TABLES ................................................... xii LIST OF FIGURES.................................................. xiv CHAPTER 1. INTRODUCTION AND BACKGROUND ......................... 1 1.1 Introduction . 1 1.2 Polymer Flammability . 2 1.3 Simulation Methods. 4 1.3.1 Reactive Simulation Techniques . 4 1.3.2 Molecular Representation . 7 1.3.3 Reactive Molecular Dynamics Simulations . 10 1.4 Outline of Dissertation . 13 2. REACTIVE SIMULATION METHODS .......................... 16 2.1 Introduction . 16 2.2 Quantum Chemical Calculations . 16 2.3 Vibrational Analysis . 19 2.3.1 Vibrational Analysis on Equilibrium Molecules . 19 2.3.2 Calculating Hessian components using forcefield descriptions . 21 2.3.3 Projecting out frequencies . 22 2.4 RxnMD: A Program for Reactive Molecular Dynamics . 23 2.4.1 RMD Methodology . 23 viii 2.4.2 The RxnMD Method . 26 2.4.3 Annealing Procedure . 33 2.4.4 Simulation Procedure . 34 2.4.5 First-order Kinetic Process Analysis Method . 35 2.5 Kinetic Monte Carlo . 36 3. RMDff: A SMOOTHLY TRANSITIONING FORCEFIELD FOR SIMULATING CHEMICAL REACTIONS ..................... 38 3.1 Introduction . 38 3.2 Computational Details . 39 3.2.1 Quantum Chemical Calculations . 39 3.2.2 MM3 Forcefield . 40 3.3 Development of Scission Reactions . 41 3.3.1 Dissociation of Bonds using MM3 Quartic Potential . 41 3.3.2 The Homolytic Scission
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