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Computational Chemistry of Non-Covalent Interaction and Its Application in Chemical Catalysis

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Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 5-2016 Computational Chemistry of Non-Covalent Interaction and its Application in Chemical Catalysis Vincent de Paul Nzuwah Nziko Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Chemistry Commons Recommended Citation Nziko, Vincent de Paul Nzuwah, "Computational Chemistry of Non-Covalent Interaction and its Application in Chemical Catalysis" (2016). All Graduate Theses and Dissertations. 5248. https://digitalcommons.usu.edu/etd/5248 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. COMPUTATIONAL CHEMISTRY OF NON-COVALENT INTERACTION AND ITS APPLICATION IN CHEMICAL CATALYSIS by Vincent de Paul Nzuwah Nziko A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Chemistry Approved: Steve Scheiner Alexander I. Boldyrev Major Professor Committee Member Alvan Hengge T.C. Shen Committee Member Committee Member Cheng-Wei Tom Chang Mark R. McLellan Committee Member Vice President for Research and Dean of the School of Graduate Studies UTAH STATE UNIVERSITY Logan, Utah 2016 ii Copyright © Vincent de Paul Nzuwah Nziko 2016 All Rights Reserved iii ABSTRACT Computational Chemistry of Non-Covalent Interaction and its Application in Chemical Catalysis by Vincent de Paul Nzuwah Nziko, Doctor of Philosophy Utah State University, 2016 Major Professor: Dr. Steve Scheiner Department: Chemistry and Biochemistry Unconventional non-covalent interactions such as halogen, chalcogen, and tetrel bonds are gaining interest in several domains including but not limited to drug design, as well as novel catalyst design. Non-covalent interactions are known as weak forces of interactions when they are considered on an individual basis, but on a molecular basis, these effects become important such that their prevalence can be seen in the construction of large biomolecules like proteins, DNA and RNA. In this work, the fundamental aspects of these interactions are looked upon using ab initio and Density Functional Theory (DFT). An essential aspect of chalcogen bonds involving Sulfur as donor atom with nitrogen, oxygen and -system as electron sources was examined. These bonds are strong with binding energy that varies from a minimum of 3 kcal/mol in some -system to 19 kcal/mol in primary amine systems. Decomposition of the total interaction energy reveals that the induction energy constitutes more than half of the total interaction energy. The shortness and strength of some of the chalcogen bond interactions suggest these interactions may in iv some cases be described as weak covalent bonds. A comparative study of -hole tetrel bonding with -hole halogen bonds in complexes of XCN (X = F, Cl, Br, I) and ammonia shows that the -hole geometry if favored for X = F, and the -hole structure is preferred for the heavier halogens. Also, the potential use of these non-covalent interactions in organic catalysis was explored. The energy barrier of the Aza-Diels-Alder reaction is substantially lowered by the introduction of an imidazolium catalyst with either a Hydrogen or halogen (X) atom in the 2-position. (269 pages) v PUBLIC ABSTRACT Computational Chemistry of Non-Covalent Interaction and its Application in Chemical Catalysis Vincent de Paul Nzuwah Nziko Known to be weaker than conventional covalent bonds, non-covalent bonds, especially hydrogen bond, has shown to be of great importance in molecular structures such as DNA, RNA, proteins and other organic frameworks. In this dissertation, we looked at non-covalent interactions other than the hydrogen bond. Replacement of the bridging hydrogen atom in a typical hydrogen bond by other atoms such a halogen, chalcogen and tetrel lead to the formation of interactions which are comparable in strength to the hydrogen bond. Unlike the hydrogen bond which arises mainly from electrostatics, these unconventional interactions mostly result from induction. Besides studying the fundamentals of these interactions, potential applications of these forces especially in organic catalysis are also explored. vi DEDICATION I would like to dedicate this work to my Family. vii ACKNOWLEDGMENTS There are many people to whom I will like to express my significant thanks for enabling me go through this stage of life and completing this work. In that respect, I would like to express my sincere gratitude to my advisor Professor Steve Scheiner for giving me a new name “Victor” also for his guidance, motivation, and advice throughout my research and study in his group. Your expertise and mentorship have enabled me to develop professional skills that will benefit me in many aspects of my career for the years to come. My thesis committee has significantly enhanced my graduate experience. In this regard, I am grateful to Dr. Alexander I. Boldyrev, Dr. Alvan Hengge, Dr. Tom Chang and Dr. T. C. Shen for their valuable suggestions, meaningful discussions, and valuable insights. Special thanks to Dr. Tapas Kar for his constant help and support during my research work. I am thankful to Binod Nepal, Upendra Adhikari, Sandra Lundell, Alex Ivanov, Timur Galeev, Ivan Popov, Nimesh Khadka and Marina Fosso for their help, camaraderie, and discussion during my studies here. I will also like to thank the Department of Chemistry and Biochemistry at Utah State University for providing me with the possibility to pursue my graduate education as well as offering me teaching assistantships. I am thankful to the Division of Research Computing in the Office of Research and Graduate Studies at Utah State University for the use of their computer and storage facilities. viii CONTENTS Page ABSTRACT ....................................................................................................................... iii PUBLIC ABSTRACT .........................................................................................................v DEDICATION ................................................................................................................... vi ACKNOWLEDGMENTS ................................................................................................ vii LIST OF TABLES ............................................................................................................. xi LIST OF FIGURES ......................................................................................................... xiv LIST OF SCHEMES...................................................................................................... xviii ABBREVIATION............................................................................................................ xix CHAPTER 1. INTRODUCTION ...................................................................................................1 References ............................................................................................................ 11 2. CHALCOGEN BONDING BETWEEN TETRAVALENT SF4 AND AMINES .18 Abstract ................................................................................................................ 18 2-1. Introduction ................................................................................................. 18 2-2. Computational Method .............................................................................. 20 2-3. Results .......................................................................................................... 21 2-4. Summary ...................................................................................................... 28 References ............................................................................................................ 31 3. INTRAMOLECULAR S∙∙O CHALCOGEN BOND AS STABILIZING FACTOR IN GEOMETRY OF SUBSTITUTED PHENYL-SF3 MOLECULES 48 Abstract ................................................................................................................ 48 3-1. Introduction ................................................................................................. 48 3-2. Methods ........................................................................................................ 52 3-3. Results and Discussion ............................................................................... 52 3-4. Conclusion ................................................................................................... 63 References ............................................................................................................ 65 ix 4. S∙∙π CHALCOGEN BOND BETWEEN SF2 or SF4 AND C-C MULTIPLE BOND ....................................................................................................................75 Abstract ................................................................................................................ 75 4-1. Introduction ................................................................................................. 75 4-2. Theoretical Methods ................................................................................... 78 4-3. Results .......................................................................................................... 79 4-4. Discussion ...................................................................................................
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