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Prediction of Molecular Crystal Structures

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Prediction of Molecular Crystal Structures Prediction of molecular crystal structures Theresa Beyer A thesis submitted to the University of London in partial fulfilment of the requirements for the degree of Doctor of Philosophy, April 2001, Centre for Theoretical and Computational Chemistry Department of Chemistry University College London 20 Gordon Street London WCIH OAJ United Kingdom ProQuest Number: 10014432 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest 10014432 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 Acknowledgements Academic acknowledgements I would like to thank my supervisor Professor Sarah L. Price for her enthusiasm and continued support over the course of my postgraduate work. It has been a great pleasure to work with her and I am grateful for her commitment and advice. Dr W. D. Sam Motherwell and Dr Jos P. M. Lommerse are thanked for collaboration, many helpful and enjoyable discussions and for organising the CCDC crystal structure prediction workshop for small organic molecules in May 1999 and the annual CCDC student days. Furthermore I would like to thank Dr Herman L. Ammon for help with the program MOLPAK and Professor Christopher S. Frampton (Roche Discovery) and Dr C. C. Wilson (CLRC Rutherford Appel ton Laboratories) for providing the unpublished atomic coordinates of many of the paracetamol crystal structures (chapter 6). Mr. Amer Ramzan, a UCL project student, is thanked for preliminary work on the crystal structure prediction of paracetamol (chapter 6). I would like to thank all past and present members of our research group for their friendship and their support, especially Dr Tanja van Mourik for her advice and help with ab initio techniques. Graeme Day and Michael Brunsteiner are thanked for an introduction into elastic properties and morphology calculations, respectively (chapter 6 and 7). I am grateful to NATO Science (Euroconference, Erice/Italy, 1998), the British Crystallographic Association (lUCr XVIIl'^ Congress and General Assembly, Glasgow/United Kingdom, 1999) and the Bursary Committee of the 19^*^ European Crystallographic Meeting (ECM19, Nancy/France, 2000) for conference grants. Finally I would like to thank the EPSRC and the Cambridge Crystallographic Data Centre for a generous Ph. D. case studentship. Acknowledgements Personal acknowledgements I would like to thank my family - especially my parents, and Michael’s family for their continued support. Michael for his talent to make me smile and much more ... Leaving a familiar place always means leaving friends behind. I would like to thank my friends for the strength and dedication to keep in touch. There are many more years to come ... All Sisters of St Philomena’s for a warm place in the heart of the city. London - for attracting people from all over the world and therefore offering a unique learning experience. It has taught me a lesson or two ... Finally, I would like to thank the UCL Graduate School, the Research Council's Graduate School and the Higher Education and Research and Development Unit (HERDU) / UCL for the non-scientific part of my postgraduate education. ______________________________________________________________________ Abstract Abstract The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would mirror a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs) are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol'^ of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3- oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy structures of paracetamol and the carboxylic acids. These provide approximate mechanical and kinetic models to refine polymorph prediction. Table of contents Table of contents Academic acknowledgements ............................................................................................2 Personal acknowledgements ..............................................................................................3 A b stra c t................................................................................................................................. 4 Table of contents..................................................................................................................5 List of tables and figures ....................................................................................................8 C hapter 0. Overview.............................................................................................................................. 12 References for chapter 0 .........................................................................................16 C hapter 1. Molecular crystals and polymorphism .........................................................................17 1.1 Molecular crystals...................................................................................... 18 1.2 The phenomenon of polymorphism .........................................................19 1.2.1 Discovery and the definition of polymorphism .........................19 1.2.2 Conformational polymorphs ........................................................ 20 1.2.3 The importance of polymorphism .............................................. 21 1.2.4 Thermodynamic stability of polymorphs ...................................23 1.2.5 Disappearing polymorphs .............................................................24 1.3 Crystal engineering .....................................................................................25 1.4 Databases of molecular crystals and their properties ............................26 1.4.1 The Cambridge Crystallographic Database (CSD) ...................26 1.4.2 The WebBook by the National Institute of Standards and Technology (NIST) ............................................................... 27 1.5 Tools for a theoretical comparison of molecular crystal structures and polymorphs ........................................................................28 1.5.1 Visual comparison......................................................................... 28 1.5.2 Graph set theory .............................................................................28 1.5.3 Reduced cells ................................................................................. 29 1.5.4 Similarity searches .........................................................................30 1.5.5 X-ray powder diagrams .................................................................30 1.5.6 Hirshfeld surfaces .......................................................................... 30 1.6 Conclusions................................................................................................. 31 References for chapter 1 ........................................................................................32 C hapter 2. The theory of intermolecular forces ..............................................................................41 2.1 Introduction.................................................................................................42 2.2 Classification of the forces between molecules..................................... 43 2.2.1 Long range contributions ..............................................................44 2.2.2 Short range contributions ..............................................................48 2.3 Models for calculating intermolecular interactions..............................
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