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Strategies for Expanding the Halogen Bonding Periodic Clemson University TigerPrints All Dissertations Dissertations 8-2008 STRATEGIES FOR EXPANDING THE HALOGEN BONDING PERIODIC TABLE AND DESIGINING COMPLEMENTARY HALOGEN/HYDROGEN BONDING SYNTHONS Hadi Arman Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Part of the Physical Chemistry Commons Recommended Citation Arman, Hadi, "STRATEGIES FOR EXPANDING THE HALOGEN BONDING PERIODIC TABLE AND DESIGINING COMPLEMENTARY HALOGEN/HYDROGEN BONDING SYNTHONS" (2008). All Dissertations. 234. https://tigerprints.clemson.edu/all_dissertations/234 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. STRATEGIES FOR EXPANDING THE HALOGEN BONDING PERIODIC TABLE AND DESIGINING COMPLEMENTARY HALOGEN/HYDROGEN BONDING SYNTHONS A Dissertation Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Chemistry by Hadi David Arman August 2008 Accepted by: William T. Pennington, Committee Chair Steven J. Stuart Jason McNeill Donald G. Vanderveer i ABSTRACT Halogen bonding is the donation of electron density from an electron donor, such as N, O, S, Se atoms, to an electron acceptor such as a dihalogen or organohalogen. This interaction plays an important role in biological systems, such as the thyroid gland and is useful in many other fields such as drug design, crystal engineering, synthetic chemistry, material science and bioinorganic chemistry. However, currently there is a lack of information for this interaction in systems involving organoiodines with sulfur and selenium electron donors. A variety of sulfur and selenium Lewis base donors were investigated with various organoiodines. The main goal of this research was to better understand how different types of Lewis base donors affected the formation and strength of halogen bonds. This study investigated two classes of sulfur and selenium donors which included; thiones and selenones and tertiary phosphine sulfides and selenides. These donors were used with a variety of organoiodine acceptors which included 1,4-diiodotetrafluorobenzene, tetraiodoethylene, 1,2-diiodotetrafluorobenzene, and iodoform. Single crystal X-ray diffraction analysis is by far the best method to study these interactions, however single crystals suitable for analysis cannot always be obtained. It has been shown that advanced algorithms such as Monte Carlo and the genetic algorithm can be used to elucidate crystal structures from X-ray powder diffraction data which would be advantageous in investigating halogen bonding. Our research focused on the application of a program, OCEANA (developed by Dr. C.W. Padgett), to elucidate ii crystal structures from X-ray powder diffraction data. This program was tested against a variety of organic molecules in different space groups to determine the effectiveness of the program. In addition to this, the crystal structure of bis(5-quinoline) diacetylene was elucidated completely from X-ray powder diffraction data. iii DEDICATION I would like to dedicate this work to my parents for their sacrifices they made for me to obtain my degree. I would also like to dedicate this work to my brother Hassan Benjamin Arman (1981-2003) and my grandfather Albert Alfred Durkee (1925-2002). iv ACKNOWLEDGMENTS First and foremost I wish to thank my research advisor Dr. William T. Pennington, for his support and guidance in the completion of my degree. Subsequently, I would like to thank my committee members: Dr. Steven J. Stuart, Dr. Jason McNeill, and Dr. Donald G. Vanderveer for their help and guidance throughout this degree and in editing and refining this manuscript. I would like to acknowledge my past undergraduate students who without their help I would not have been able to solve so many crystal structures. They include: Jonathan D. Buck, Sarah Dunaway, Sarah Hill, Josh Kimery, Christopher Louviere, Rebecca Glanville, and Joe Smoak. I would also like to thank Dr. Dorota Abramovitch for help in synthesizing the bis(diphenylphosphine chalcogenides) n-alkanes and her pertinent discussion on organic chemistry. Finally, I would like to thank my parents Farshad and Sandra Arman, for the support throughout the years. Also like to thank Sawsan Zainal for her support and encouragement in helping me finish my dissertation. v TABLE OF CONTENTS Page TITLE PAGE........................................................................................................................i ABSTRACT........................................................................................................................ii DEDICATION...................................................................................................................iii ACKNOWLEDGMENTS..................................................................................................iv LIST OF TABLES...........................................................................................................viii LIST OF FIGURES............................................................................................................ix CHAPTER I. INTRODUCTION.............................................................................................1 Halogen Bonding.........................................................................................1 History..............................................................................................1 Description.......................................................................................3 Previous Studies...............................................................................3 Techniques for Elucidating Crystal Structures..........................................11 Introduction....................................................................................11 Methods..........................................................................................12 Conclusion................................................................................................15 References................................................................................................16 II. HALOGEN BONDED COMPLEXES OF Ph3PSe.........................................22 Introduction................................................................................................22 Halogen Bonded Complexes......................................................................23 Ph3PSe • TIE..................................................................................23 Ph3PSe • 1,4 F4DIB .......................................................................30 Ph3PSe • 1,2-F4DIB.......................................................................30 Comparison to Known Seleno- Halogen Bonded Complexes...................32 Phenyl Embraces........................................................................................39 Thermal Analysis.......................................................................................42 Conclusion.................................................................................................46 References..................................................................................................47 vi Table of Contents (Continued) Page III. HALOGEN BONDED COMPLEXES OF BENZIMIDAZOLES................50 Introduction................................................................................................50 Halogen Bonded Complexes......................................................................51 MBZIM • 1,4 F4DIB.......................................................................51 MMBZIM • 1,4 F4DIB....................................................................55 MBZOX and MBZTH • 1,4 F4DIB.................................................58 MBZIM • 1,2 F4DIB........................................................................61 MBZOX • 1,2 F4DIB.......................................................................61 MBZIM • TIE..................................................................................67 MBZTH • TIE..................................................................................70 MBZTH • CH3I................................................................................70 Conclusion.................................................................................................74 References.................................................................................................78 IV. SOLVATED STRUCTURES OF DIPHENYLDITHIOGLYCOURIL.......80 Introduction...............................................................................................80 DPDTGU and Solvates.............................................................................82 DPDTGU........................................................................................82 DPDTGU • PYR and DPDTGU • THF...........................................82 DPDTGU • DMF.............................................................................86 Thermal and PXRD Analysis...................................................................90 Conclusion...............................................................................................93 References................................................................................................94 V. HALOGEN BONDED COMPLEXES OF DIPHENYLDITHIOGLYCOURIL...............................................................96
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