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Computational Investigation of the Sn2 Reactivity of Halogenated Pollutants

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Computational Investigation of the Sn2 Reactivity of Halogenated Pollutants COMPUTATIONAL INVESTIGATION OF THE SN2 REACTIVITY OF HALOGENATED POLLUTANTS A DISSERTATION SUBMITTED TO THE DEPARTMENT OF CIVIL AND ENVIRONMENTAL ENGINEERING AND THE COMMITTEE OF GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Brett Taketsugu Kawakami December 2010 © 2011 by Brett Taketsugu Kawakami. All Rights Reserved. Re-distributed by Stanford University under license with the author. This dissertation is online at: http://purl.stanford.edu/cs274qq3228 ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Martin Reinhard, Primary Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Lynn Hildemann I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. James Leckie Approved for the Stanford University Committee on Graduate Studies. Patricia J. Gumport, Vice Provost Graduate Education This signature page was generated electronically upon submission of this dissertation in electronic format. An original signed hard copy of the signature page is on file in University Archives. iii Table of Contents Abstract............................................................................................................................. iv Acknowledgements ........................................................................................................... v Table of Contents ............................................................................................................. vi List of Tables .................................................................................................................... xi List of Figures.................................................................................................................xiii List of Abbreviations ...................................................................................................... xv 1 Introduction............................................................................................................... 1 1.1 Motivation........................................................................................................... 1 1.2 Objectives ........................................................................................................... 2 1.3 Nucleophilic Substitution Reactions................................................................... 2 1.4 Previous Efforts to Understand Reactivity of Halogenated Pollutants............... 3 1.4.1 Limitations of Experimental Interpretation ................................................ 3 1.4.2 The Role of Solvent .................................................................................... 4 1.4.3 The Advent of Computational Studies........................................................ 4 1.5 Research Overview ............................................................................................. 5 1.6 Halogenated Compounds of Potential Environmental Significance................... 6 2 SN2 Reactivity of Halogenated Compounds ........................................................... 8 2.1 Reaction Environments....................................................................................... 9 2.1.1 Solution/Hydrolysis .................................................................................... 9 2.1.2 Biological Transformations ...................................................................... 10 2.1.3 Gas Phase.................................................................................................. 10 2.2 Previous Investigations of SN2 Reactivity ........................................................ 11 2.2.1 Hydrolysis................................................................................................. 11 2.2.2 Biological Transformations ...................................................................... 17 2.2.3 Gas Phase Studies ..................................................................................... 19 2.2.4 Theoretical Studies....................................................................................20 2.3 SN2 Reaction Profile ......................................................................................... 21 2.4 SN2 Transformation Rates................................................................................. 24 2.4.1 Empirical – Arrhenius Equation ............................................................... 24 2.4.2 Statistical Rate Theory – Eyring Polyani Equaton ................................... 25 2.5 Existing Haloalkane Structure-Reactivity Understanding................................ 25 2.5.1 Nature of Effects....................................................................................... 26 2.5.2 Structural Features .................................................................................... 26 2.5.3 Solvent Effects.......................................................................................... 29 2.6 Theories of SN2 Reactivity................................................................................ 30 2.6.1 Valence Bond Configuration Mixing Model (VBCM)............................. 31 2.6.2 Ab Initio Methods – Molecular Orbital Theory........................................ 32 3 Research Approach................................................................................................. 33 3.1 Approach........................................................................................................... 33 3.1.1 Calculation of Activation Energies (Chapter 5)........................................ 33 3.1.2 Development of SRRs (Chapter 5) ........................................................... 34 vi 3.1.3 Identification of Mechanisms (Chapter 6) ................................................ 34 3.1.4 Docking Studies (Chapter 7)..................................................................... 34 3.1.5 Quantum Chemical Based QSAR Models for Hydrolysis and Biological Data (Chapter 8)........................................................................................................ 35 3.2 Hypotheses to be tested..................................................................................... 35 3.3 Relationship of Gas Phase Activation Energies to Environmental Transformation Rates.................................................................................................... 36 3.4 Nucleophiles Included in the Study .................................................................. 38 3.5 Compound Set................................................................................................... 38 4 Methods.................................................................................................................... 42 4.1 Ab Initio Methods............................................................................................. 42 4.1.1 The Hamiltonian ....................................................................................... 42 4.1.2 Solution of the Schröedinger Equation..................................................... 43 4.1.3 Gaussian 98 Calculations.......................................................................... 44 4.2 AUTODOCK .................................................................................................... 47 4.2.1 Energy Evaluation..................................................................................... 47 4.2.2 Monte Carlo Simulated Annealing ........................................................... 47 4.2.3 AUTODOCK simulations......................................................................... 48 5 Ab Initio Calculations and Structure Reactivity Relationship (SRR) Development .................................................................................................................... 55 5.1 Results............................................................................................................... 55 5.2 Structure Reactivity Relationships for Govr .................................................... 58 5.2.1 Leaving Group Effects.............................................................................. 59 5.2.2 Chain Length............................................................................................. 61 5.2.3 substituent effects.................................................................................. 62 5.2.4 substituent effects .................................................................................. 65 5.2.5 Vinyl groups..............................................................................................69 5.2.6 Cyclic groups............................................................................................ 69 5.2.7 Other Observations................................................................................... 70 5.3 Solvent Effects.................................................................................................. 73 5.4 Other Nucleophiles........................................................................................... 75 5.5 Summary of Structure Reactivity Relationships............................................... 75 5.6 Implications for Experimental Interpretation...................................................
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