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The Role of Halogen Bonding in Biomolecules

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The Role of Halogen Bonding in Biomolecules THE ROLE OF HALOGEN BONDING IN BIOMOLECULES Simon William Leslie Hogan A Thesis Submitted for the Degree of PhD at the University of St Andrews 2018 Full metadata for this item is available in St Andrews Research Repository at: http://research-repository.st-andrews.ac.uk/ Please use this identifier to cite or link to this item: http://hdl.handle.net/10023/13840 This item is protected by original copyright The Role of Halogen Bonding in Biomolecules Simon William Leslie Hogan This thesis is submitted in partial fulfilment for the degree of Doctor of Philosophy (PhD) at the University of St Andrews March 2018 Abstract This study concerns halogen bonding between small molecules. Except where otherwise stated herein this investigation was performed exclusively using the M06-2X density functional, in conjunction with the 6-31+G* basis set except for iodine and astatine which were treated using the aug-cc-pVDZ-PP basis set with relativistic pseudopotentials. All calculations were performed in the gas phase. The counterpoise procedure was employed for all full geometry optimisations. Statistical analysis of the Cambridge Structural Database, wherein the frequency of structures as a function of halogen bond angle and distance constituted the sole part of this study not to be based on density functional theory. Except in chapter 5, all halogens from fluorine to astatine are investigated. In chapter 3, halogen bonding between halobenzene and a single water molecule is discussed. Competition between R – X•••OH2 halogen bonding and R – X•••H-O-H hydrogen bonding interactions is described. This system is analogous to the more elaborate microsolvated 1- methyl-5-halouracil system described in chapter 4. In this latter system one 1-methyl-5- halouracil molecule interacts with either one or two water molecules. A central feature of the investigation into this system is competition between R – X•••OH2 and R=O•••H-O-H hydrogen bonding. In chapter 5, halogen bonding is discussed in the context of the thyroid system. In particular halogen bonding between a thyroxine iodine atom and the protein backbone as well as crystal water molecules is the subject of this chapter. The effect of substitution of the iodine atom with an astatine atom is presented. Chapter 6 is concerned with halogen bonding in halogenated DNA base pairs. Interaction energies are compared with those of the canonical base pairs, and the effect of halogen bonding on geometry is also discussed. For each system, halogen bonding was found to become stronger and more tolerant of non- linear bond angles going down the halogen group. i Declarations Candidate's declaration I, Simon William Leslie Hogan, do hereby certify that this thesis, submitted for the degree of PhD, which is approximately 50,000 words in length, has been written by me, and that it is the record of work carried out by me, or principally by myself in collaboration with others as acknowledged, and that it has not been submitted in any previous application for any degree. I was admitted as a research student at the University of St Andrews in September 2013. I confirm that no funding was received for this work. Date Signature of candidate Supervisor's declaration I hereby certify that the candidate has fulfilled the conditions of the Resolution and Regulations appropriate for the degree of PhD in the University of St Andrews and that the candidate is qualified to submit this thesis in application for that degree. Date Signature of supervisor Permission for publication In submitting this thesis to the University of St Andrews we understand that we are giving permission for it to be made available for use in accordance with the regulations of the University Library for the time being in force, subject to any copyright vested in the work not being affected thereby. We also understand, unless exempt by an award of an embargo as requested below, that the title and the abstract will be published, and that a copy of the work may be made and supplied to any bona fide library or research worker, that this thesis will be electronically accessible for personal or research use and that the library has the right to migrate this thesis into new electronic forms as required to ensure continued access to the thesis. I, Simon William Leslie Hogan, confirm that my thesis does not contain any third-party material that requires copyright clearance. ii The following is an agreed request by candidate and supervisor regarding the publication of this thesis: Printed copy Embargo on all of print copy for a period of 2 years on the following ground(s): • Publication would preclude future publication Supporting statement for printed embargo request There is an intention to publish the work in the form of journal articles. The majority of the thesis has not yet been published. Electronic copy Embargo on all of electronic copy for a period of 2 years on the following ground(s): • Publication would preclude future publication Supporting statement for electronic embargo request There is an intention to publish the work in the form of journal articles. The majority of the thesis has not yet been published. Title and Abstract • I agree to the title and abstract being published. Date Signature of candidate Date Signature of supervisor iii Underpinning Research Data or Digital Outputs Candidate's declaration I, Simon William Leslie Hogan, hereby certify that no requirements to deposit original research data or digital outputs apply to this thesis and that, where appropriate, secondary data used have been referenced in the full text of my thesis. Date Signature of candidate iv Acknowledgements General acknowledgements I wish to thank my supervisor, Dr. Tanja van Mourik for providing me with support and guidance throughout my Ph.D., which has been indispensable in enabling me to produce this work. I would like to express my appreciation for Rachael Skyner’s assistance to me in relation to the statistical analysis contained in chapter 4. Furthermore, I am grateful to everyone with whom I have interacted in room 150. Most of the calculations in this work were performed on the Wardlaw computing cluster via the EaStCHEM Research Computing Facility, while the remainder were performed on the Obelix cluster. Both of these clusters are maintained by Dr. Herbert Füchtl. v Contents Abstract ........................................................................................................................................ i Declarations ............................................................................................................................... ii Acknowledgements ................................................................................................................... v Contents ......................................................................................................................................vi List of Abbreviations ................................................................................................................. ix 1 Introduction ............................................................................................................................ 1 2 Background theory to the computational methods employed in the present investigation ............................................................................................................................. 12 2.1 Schrödinger equation ........................................................................................................ 12 2.2 Born-Oppenheimer approximation ................................................................................... 13 2.3 Hartree-Fock theory .......................................................................................................... 13 2.4 Post Hartree-Fock methods .............................................................................................. 15 2.4.1 Second order Møller-Plesset perturbation theory ..................................................... 15 2.5 Basis sets ........................................................................................................................... 16 2.5.1 A note of caution ........................................................................................................ 17 2.5.2 6-31+G* ...................................................................................................................... 17 2.6 Relativistic effective core potentials ................................................................................. 17 2.6.1 aug-cc-pVDZ-PP .......................................................................................................... 18 2.7 BSSE and the counterpoise correction procedure ............................................................ 18 2.8 Density functional theory .................................................................................................. 19 2.8.1 The Hohenberg-Kohn theorems ................................................................................. 19 2.8.2 Kohn-Sham Method ................................................................................................... 20 2.8.3 Jacob’s ladder ............................................................................................................. 21 2.8.4 Empirical parameterisation for dispersion effects ..................................................... 23 2.8.5 M06-2X ......................................................................................................................
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