CHAPTER 4 Neutron Diffraction Studies of 2

$CHAPTER 4 Neutron Diffraction Studies of 2$ Durham E-Theses Weak intermolecular interactions in organic systems: a concerted study involving x-ray and neutron diraction and database analysis Hoy, Vanessa J. How to cite: Hoy, Vanessa J. (1996) Weak intermolecular interactions in organic systems: a concerted study involving x-ray and neutron diraction and database analysis, Durham theses, Durham University. Available at Durham E-Theses Online: http://etheses.dur.ac.uk/5304/ Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in Durham E-Theses • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full Durham E-Theses policy for further details. Academic Support Oce, Durham University, University Oce, Old Elvet, Durham DH1 3HP e-mail: [email protected] Tel: +44 0191 334 6107 http://etheses.dur.ac.uk 2 Weak Intermolecular Interactions in Organic Systems: A Concerted Study Involving X-ray and Neutron Diffraction and Database Analysis. Vanessa J. Hoy Thesis submitted in part fulfilment of the requirements for the degree of Doctor of Philosophy at the University of Durham The copyright of this thesis rests with the author. No quotation from it should be pubUshed without his prior written consent and information derived from it should be acknowledged. Department of Chemistry 1 0 MAR 1997 October 1996 Weak Intermolecular Interactions in Organic Systems: A concerted Study Involving X-ray and Neutron Diffraction and Database Analysis. Submitted for the degree of Doctor of Philosophy, October 1996, by Vanessa J. Hoy, University of Durham ABSTRACT This thesis can be divided broadly into two halves. The first half (Chapters 3 - 5) deals with crystallographic studies of compounds which contain weak intermolecular interactions or networks of these interactions. Whilst the later part (Chapters 7 - 9) describes the results of database surveys of three novel weak intermolecular interactions. In Chapters 3 and 4 the neutron derived structures of 3,5-dinitrocinnamic acid, 2-ethynyladamantan-2-ol, 2- and 3-aminophenol are presented. All of the compounds contain complex networks of weak hydrogen bonds. The neuron diffraction data are used to determine accurate hydrogen atom poistions and thus characterise these hydrogen bonded networks. Some theoretical work is also described. In Chapter 5, X-ray diffraction studies of a series of iodobenzene derivatives are described. These compounds were synthesised in an attempt to engineer structures mediated by novel X...O2N interactions. The structures of three iodo nitrobenzenes are presented wherein symmetrical bifurcated I...O2N interactions mediate the primary ribbon motif. The structure of TCNQ derivative, in which I...N=C play a structure determining role, is also described. Chapters 7, 8 and 9 describe database studies of X...O2N, C(ring)-H...O/N and C-F...H interactions. The frequencies and geometries of the interactions were determined and analysed. The data for X...O2N interactions were used in conjunction with sophisticated IMPT calculations to determine prefered interaction geometries and interaction energies. Similar theoretical techniques were used to analyse the C(ring)-H...O/N and C-F..H interactions described in Chapters 8 and 9. Background information and overviews of the general experimental procedures followed when performing the crystallographic and database studies are given in Chapters 2 and 6. u DECLARATION The work described in this thesis was carried out in the Department of Chemistry at the University of Durham between October 1993 and September 1996, under the supervision of Prof. Judith A. K. Howard. All the work is my own, unless otherwise stated, and has not been submitted previously for a degree at this, or any other university. Vanessa J. Hoy The copyright of this thesis rests with the author. No quotation from it should be published without her prior written consent and information derived from it should be acknowledged. m ACKNOWLEDGEMENTS First of all I would like to thank my supervisor. Prof. Judith Howard and the co- supervisors of the project, Dr. Frank Allen and Prof. Gautam Desiraju for the help, support and encouragement they have provided throughout the three years. I must also thank Prof. Desiraju and his students in Hyderabad for supplying all of the crystals used for the work described here. The efforts of my local contacts at ISIS and the ILL, Dr. Chick Wilson and Dr. Garry Mclntyre are very much appreciated and I would particularly like to thank Chick for the time he spent proof reading sections this thesis. My colleagues, past and present, in Durham and at the CCDC have provided a vast amount of practical help and emotional support during the last three years. In particular I would like to thank: Dr. Roy Copley, Dr. Christian Lehmann, Dr. Jason Cole and Dr. Claire Wilson for teaching me what little I know about crystallography; Dr. Scott Rowland, Dr. Ian Bruno and Dr. Neil Stewart for providing the solutions to my problems with the CSDS and related software; and Mark Roden, Jacqui Cole, Pete Ford, Stephanie Hull, and Roy for taking me to the pub when things were bad and going to the pub with me when things were good. Finally, I want to thank my Mends outside of work for giving me the opportunity to take a breather now and again. In particular Dena Bellamy, Juliette Cook, Susie Dalton, Gill Thompson, Alison Sykes, Paula Rudkin, Monika Lauterbach, Irene Higler and all of the members of DUWHC past and present. Your support means a great deal. IV TABLE OF CONTENTS Title i Abstract ii Declaration iii Acknowledgements iv Table of Contents v List of Figures xii List of Tables xvi List of Abbreviations xx Chapter 1 - Introduction 1.1 Intermolecular Interactions 2 1.2 Crystallographic Investigations of Weak Intermolecular Interactions 3 1.2.1 Neutron Diffraction 3 1.2.2 X-ray Diffraction 4 1.2.3 Database Analysis 4 1.3 Scope of this Thesis 6 1.4 References 9 Chapter 2 - Diffraction, X-rays, Neutrons and SXD 2.1 Single Crystal Diffraction 12 2.1.1 Bragg'sLaw 12 2.1.2 X-rays as Atomic Probes 13 2.2 X-ray Diffraction Experiments 15 2.2.1 Crystal Selection and Mounting 16 2.2.2 Indexing 17 2.2.3 Data Collection 19 2.2.4 Data Reduction 21 2.2.4.1 The Lorentz Correction 22 2.2.4.2 The Polarisation Correction 22 2.2.4.3 The Absorption Correction 22 2.2.4.4 The Decay Correction 24 2.2.4.5 The Extinction Correction 24 2.2.5 Space Group Determination 26 2.2.6 Structure Solution 27 2.2.7 Stiiictiire Refinement 29 2.3 Neuti-on Diffraction 31 2.3.1 Neutrons as Atomic Probes 31 2.3.1.1 Neutron Sources 32 2.3.1.2 Neutron Detectors 35 2.3.2 Advantages and Disadvantages of Neutrons 36 2.4 SXDatlSIS 38 2.4.1 The ISIS Proton Spallation Source 38 2.4.2 SXD 39 2.4.3 An Overview of SXD Experimental Procedure 43 2.4.3.1 Crystal Selection and Mounting 43 2.4.3.2 Data Collection Methodology and Initial Indexing 43 2.4.3.3 Data Reduction 44 2.5 References 46 Chapter 3 - Neutron Diffraction Studies of 3,5-Dinitrocinnamic Acid and 2-Ethynyladamantan-2-oI. 3.1 Introduction 49 3.1.1 3,5-Diniti-ocinnamic Acid 49 3.1.2 2-Ethynyladamantan-2-ol 50 3.2 Experimental Details 53 3.2.1 Preliminary Studies 53 3.2.1.1 Low Temperature Stability 53 VI 3.2.1.2 Crystal Quality 54 3.2.2 Crystal Selection and Mounting 55 3.2.3 Data Collection and Indexing 57 3.2.3.1 Data Collection and Indexing for 3,5-Dinitrocinnamic Acid 57 3.2.3.2 Data Collection and Indexing for 2-Ethynyladamantan-2-ol 59 3.2.4 Data Processing and Structure Refinement 59 3.2.4.1 Processing and Refinement for 3,5-Dinitrocinnamic Acid 60 3.2.4.2 Processing and Refinement for 2-Ethynyladamantan-2-ol 60 3.3 The Structure of 3,5-Dimtrocinnamic Acid 61 3.3.1 Structural Details 61 3.3.2 The C-H...0 Bond Network 62 3.3.3 Theoretical Calculations 67 3.4 The Structure of 2-Ethynyladamantan-2-ol 72 3.4.1 Structural Details 72 3.4.2 The Hydrogen Bonded Network 74 3.5 Conclusions 78 3.6 References 79 Chapter 4 - Neutron Diffraction Studies of 2- and 3-Aminophenoi 4.1 Introduction 82 4.1.1 Alcohol-Amine Recognition 82 4.1.2 Aromatic Amine Pyramidalization 85 4.1.3 Aims 88 4.2 Experimental Details 89 4.2.1 Preliminary Studies 91 4.2.2 2-Aminophenol 91 4.2.3 3-Aminophenol 94 4.3 The Neutron Structtires of 2- and 3-Aminophenol 96 4.3.1 Structural Details 96 4.3.2 The Hydrogen Bonded Networks 99 vu 4.4 Conclusions 104 4.5 References 105 Chapter 5 - X-ray Diffraction Studies of Compounds Engineered to Contain Nitro Oxygen...Iodine Interactions 5.1 Introduction 108 5.2 Experimental Details 111 5.3 Structural Results 113 5.3.1 1:1 Co-crystal of 1,4-Diiodobenzene and 1,4-Dinitrobenzene (II) 113 5.3.2 4-Iodoniti:obenzene (m) 116 5.3.3 l:2Co-crystalof l,4-Dinitrobenzeneand4-Iodocinnamic Acid(IV) 118 5.3.4 1:1 Co-crystal of 1,4-Diiodobenzene and TCNQ (V) 122 5.4 Conclusions 126 5.5 References 127 Chapter 6 - The Cambridge Structural Database 6.1 Inti-oduction 129 6.1.1 An Historical Perspective 129 6.1.2 The Cambridge Structtu^ Database System 130 6.2 Components of die CSDS 132 6.2.1 Structural Data 132 6.2.2 Software 134 6.3 Research Applications of die CSDS 137 6.3.1 Crystallographic Studies 137 6.3.2 Mean Molecular Dimensions 137 6.3.3 Conformational Analysis 137 6.3.4 Reaction Pathways 138 6.3.5 Non-bonded

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