Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 5-2016 Quantum Mechanical Studies of Charge Assisted Hydrogen and Halogen Bonds Binod Nepal Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Biochemistry Commons, and the Chemistry Commons Recommended Citation Nepal, Binod, "Quantum Mechanical Studies of Charge Assisted Hydrogen and Halogen Bonds" (2016). All Graduate Theses and Dissertations. 5027. https://digitalcommons.usu.edu/etd/5027 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]. QUANTUM MECHANICAL STUDIES OF CHARGE ASSISTED HYDROGEN AND HALOGEN BONDS by Binod Nepal A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Chemistry Approved: Steve Scheiner Yujie Sun Major Professor Committee Member Alexander I. Boldyrev T.C. Shen Committee Member Committee Member David Farrelly 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 © Binod Nepal 2016 All Rights Reserved iii ABSTRACT Quantum Mechanical Studies of Charge Assisted Hydrogen and Halogen Bonds by Binod Nepal, Doctor of Philosophy Utah State University, 2016 Major Professor: Dr. Steve Scheiner Department: Chemistry and Biochemistry This dissertation is mainly focused on charge assisted noncovalent interactions specially hydrogen and halogen bonds. Generally, noncovalent interactions are only weak forces of interaction but an introduction of suitable charge on binding units increases the strength of the noncovalent bonds by a several orders of magnitude. These charge assisted noncovalent interactions have wide ranges of applications from crystal engineering to drug design. Not only that, nature accomplishes a number of important tasks using these interactions. Although, a good number of theoretical and experimental studies have already been done in this field, some fundamental properties of charge assisted hydrogen and halogen bonds still lack molecular level understanding and their electronic properties are yet to be explored. Better understanding of the electronic properties of these bonds will have applications on the rational design of drugs, noble functional materials, catalysts and so on. In most of this dissertation, comparative studies have been made between charge and neutral noncovalent interactions by quantum mechanical calculations. The iv comparisons are primarily focused on energetics and the electronic properties. In most of the cases, comparative studies are also made between hydrogen and halogen bonds which contradict the long time notion that the H-bond is the strongest noncovalent interactions. Besides that, this dissertation also explores the long range behavior and directional properties of various neutral and charge assisted noncovalent bonds. (396 pages) v PUBLIC ABSTRACT Quantum Mechanical Studies of Charge Assisted Hydrogen and Halogen Bonds by Binod Nepal, Doctor of Philosophy Utah State University, 2016 Major Professor: Dr. Steve Scheiner Department: Chemistry and Biochemistry Like cement bridges one brick to another, noncovalent forces also bridge two or more molecules together to form a molecular crystal or molecular cluster. Although weaker than the covalent bond, the existence of noncovalent forces can be seen everywhere from liquid water to construction of complex biomolecules like DNA, RNA, proteins etc. An introduction of suitable charge; positive or negative, on the binding units can increase the strength of noncovalent interaction by several orders of magnitude. The primary aim of this dissertation is to explore some fundamental properties of such charge assisted noncovalent interactions which will be helpful for the rational design of molecular crystals, drugs, catalysts and many more. Besides that, this dissertation also makes parallel study between H-bond and halogen bonds and contradicts the long time notion that the H-bond is the strongest noncovalent interaction. (396 pages) vi DEDICATION I would like to dedicate this work to my son Yubin. vii ACKNOWLEDGMENTS It is giving me a very joyous feeling as well as immense pleasure while writing this important section of my dissertation which I cannot express in words. It is also giving me a very nice flashback of all the time that I spent here in Utah State University. I am remembering all those people whose immense help, support, love and care were vital for the completion of this dissertation. First of all, I would like to express my deepest gratitude to my advisor Professor Steve Scheiner for his unceasing reinforcement, immense knowledge, expert guidance and motivation throughout my research and study. Had there not been the proper guidance, persistent help and inspiration, I would not be able to present my dissertation in this shape. His knowledge, encouragement and support have been instrumental in becoming a better student, researcher and a good human being. Next, I am grateful to my supervising committee members Dr. Alexander I. Boldyrev, Dr. David Farrelly, Dr. Yujie Sun and Dr. T. C. Shen for their valuable suggestions, important discussions and precious insights. Dr. Boldyrev also provided me a deep knowledge in spectroscopy and quantum mechanics with his two courses in physical chemistry. I am equally grateful to Dr. Tapas Kar for his constant help and support during my research work. Dr. Kar always helped me whenever I ended up with some technical difficulties. viii I am thankful to my colleagues and friends Dr. Upendra Adhikari and Vincent Nziko for their wonderful companionship, useful suggestions and important discussions. I would also like to thank our Nepali community in Logan, Utah especially Ramji Acharya, Kshitij Parajuli, Dr. Jaya P. Shrestha and Nimesh Khadka; you guys were wonderful for helping to find home away from home in the US. I would also like to thank Department of Chemistry and Biochemistry, Utah State University for providing me the opportunity to pursue my graduate study as well as providing teaching assistantships. I am very grateful to Office of Research and Graduate Studies at Utah State University for providing dissertation enhancement fund. Computer, storage, and other resources from the Division of Research Computing in the Office of Research and Graduate Studies at Utah State University are gratefully acknowledged. Finally, I am grateful to my parents and siblings for their constant care, love and support. The enormous love and care from my wife Yashoda will never be forgotten. Binod Nepal ix CONTENTS Page ABSTRACT ....................................................................................................................... iii PUBLIC ABSTRACT ........................................................................................................ v DEDICATION ................................................................................................................... vi ACKNOWLEDGMENTS ................................................................................................ vii LIST OF TABLES ........................................................................................................... xiv LIST OF FIGURES ....................................................................................................... xviii LIST OF SCHEMES...................................................................................................... xxiv LIST OF ABBREVIATIONS ......................................................................................... xxv CHAPTER 1. INTRODUCTION .................................................................................................... 1 References ............................................................................................ 11 2. EFFECT OF IONIC CHARGE UPON THE CH∙∙π HYDROGEN BOND ........... 18 Abstract ................................................................................................ 18 2-1. Introduction ................................................................................... 18 2-2. Computational Methods ................................................................ 22 2-3. Results ........................................................................................... 22 2-3.1. CHF3 as proton donor .................................................... 22 2-3.2. N(CH3)3 donor ............................................................... 27 + 2-3.3. N(CH3)4 donor .............................................................. 30 + 2-3.4. NH4 donor .................................................................... 33 2-3.5. NMR Chemical Shifts .................................................... 35 2-4. Summary and Discussion ............................................................. 36 References ............................................................................................ 42 x Tables and Figures ............................................................................... 54 3. ANIONIC CH∙∙X- HYDROGEN BONDS. ORIGIN OF THEIR STRENGTH, GEOMETRY, AND OTHER PROPERTIES ................................. 70 Abstract ...............................................................................................