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Probing the Solubility of Selected Nanoscale Building Blocks PROBING THE SOLUBILITY OF SELECTED NANOSCALE BUILDING BLOCKS USING MOLECULAR SIMULATION By Patrick Scott Redmill Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOPSOPHY in Chemical Engineering December, 2008 Nashville, TN Approved: Peter T. Cummings Clare McCabe Scott Guelcher Eugene LeBoeuf M. Douglas LeVan To Mom and Dad SUPPORT LOCAL COLLEGE RADIO WRVU 91.1 FM ii ACKNOWLEDGEMENTS This work has been possible through the financial support of the National Science Foundation. Additionally, the simulations in this work were done using the computational resources at NERSC and ACCRE. I am grateful for the support, guidance, and patience I have received during my research from my advisors, Professor Peter T. Cummings and Clare McCabe. I would also like to thank the members of my Dissertation Committee for their time, valuable insights, and unique observations that they contributed to this work. Vanderbilt University, as a whole, deserves great thanks as well. I am very grateful for the exposure to some of the best educators in world that Vanderbilt provided. I truly consider Vanderbilt my academic home. I would like to thank Dr. Alberto Striolo, who was absolutely instrumental in initiating me to this work. Shannon Capps is also due special thanks for all of her hard work (i.e. things I didn’t want to do and passed off on a poor undergrad) while a student in the McCabe lab. Finally, I would like to thank my lab mates, in particular, Christina Payne, Peter Dyer, and Hugh Docherty. Without their daily perspective, humor, coffee breaks and lunch breaks, I would have killed somebody over all this. iii TABLE OF CONTENTS Page DEDICATION…………………………………………………………………....………...…ii ACKNOWLEDGEMENTS…………………………………………………...……………iii LIST OF TABLES…………………………………………………………………….…...vii LIST OF FIGURES…………………………………………………………………….…...ix Chapter I. INTRODUCTION .............................................................................................................1 References ................................................................................................................ ...15 II. BACKGROUND & THEORY ....................................................................................... 22 General Methodology .................................................................................................. 22 Thermodynamic integration and solubility calculations............................................ 24 Calculation of UNIFAC Group-Contribution Parameters and Activity Coefficients ..... 33 Lipid Bilayer Perturbation Studies............................................................................ 37 References ................................................................................................................... 40 III. ON THE CALCULATION OF THE GIBBS FREE ENERGY OF SOLVATION FOR FULLERENE PARTICLES BY MOLECULAR DYNAMICS SIMULATIONS........... ......43 Introduction ................................................................................................................. 43 Simulation Details.................................................................................................... 45 Results and Discussion................................................................................................. 51 Fullerenes in Water Solvent.................................................................................... .51 Fullerenes in Octanol Solvent.................................................................................. 57 Conclusion................................................................................................................... 60 References ................................................................................................................... 61 IV. ESTIMATING INFINITELY DILUTE ACTIVITY COEFFICIENTS FOR SELECTED NANOPARTICLES USING GROUP-CONTRIBUTION METHODS AND AB INITIO CALCULATIONS.............................................................................................................. 66 Introduction ................................................................................................................. 66 Methodology............................................................................................................ 69 iv The UNIFAC group-contribution model.................................................................. 69 Ab Initio calculations............................................................................................... 71 Thermodynamic integration technique..................................................................... 74 Results and Discussion................................................................................................. 79 Application of ab initio supermolecule/UNIFAC method of computing KO/W for alkanes and alcohol.................................................................................................. 79 Application of UNIFAC to C60 in octanol and water systems ................................... 82 UNIFAC/supermolecule analysis of H-POSS and water/octanol systems................. 83 Calculation of ΔGsolv for benzene in water using Mulliken Charges ….…….…...…. 83 Solubility response associated with adding hydrophilic groups using thermodynamic integration and UNIFAC …………………………………………..…….....…...…… …………………………………………………………………..…………………....85 Conclusions ................................................................................................................. 88 References ................................................................................................................... 89 V. BEHAVIOR OF SELECTED NANOSCALE BUILDING BLOCKS IN A LIPID BILAYER: A MOLECULAR DYNAMIC STUDY................................................................. ..................................................................................................................................................95 Introduction ................................................................................................................. 95 Simulation Details ....................................................................................................... 99 Results and Discussion............................................................................................... 103 Study of C60 in DPPC............................................................................................. 104 Study of J-POSS in DPPC..................................................................................... 107 Conclusions ............................................................................................................... 110 References ................................................................................................................. 111 VI. CONCLUSION AND FUTURE WORK.......................................................................117 Conclusions ............................................................................................................... 117 Future Work .............................................................................................................. 118 CHARMM parameterization for fullerene materials .............................................. 118 UNIFAC parameterization of bare NBB units........................................................ 120 References ................................................................................................................. 120 APPENDIX A: ELECTRONIC STRUCTURE CALCULATIONS.....................................122 General Formulism .................................................................................................... 122 Levels of Theory ....................................................................................................... 127 Hartree-Fock ........................................................................................................ 127 Density Functional Theory.……………………….…………………..………….…129 Møller-Plesset Perturbation Theory ....................................................................... 131 Electronic Structure Parameterization Techniques...................................................... 132 Mulliken Population Analysis................................................................................ 132 Counterpoise Correction........................................................................................ 133 References ................................................................................................................. 134 v APPENDIX B: FUNDAMENTAL TOOLS FOR BULK MD SIMULATIONS..................133 Ewald Summation...................................................................................................... 136 Fourier Contribution to Ewald Sum ....................................................................... 136 Correction for self-interaction................................................................................ 138 Real space term ..................................................................................................... 140 Nosé-Hoover thermostat/barostat........................................................................... 140 References………………………………...…………………………………..….…142 APPENDIX C: C60(OH)32 OPTIMIZED STRUCTURE ………………………..…..……143 APPENDIX D: SAMPLE INPUT DL_POLY TI input files……………………………………….…………………..……..145 CONTROL …………………………………………………………………..……..145 FIELD…………………...…………....….……...……………………..……..……..146
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