Discovering Conglomerates for Chiral Resolution by Crystallization Aliou Mbodji To cite this version: Aliou Mbodji. Discovering Conglomerates for Chiral Resolution by Crystallization. Cristallography. Normandie Université, 2020. English. NNT : 2020NORMR006. tel-02917352 HAL Id: tel-02917352 https://tel.archives-ouvertes.fr/tel-02917352 Submitted on 19 Aug 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈ SE Pour obtenir le diplôme de doctorat Spécialité Chimie Préparée au sein de l’Université de Rouen Normandie Discovering Conglomerates for Chiral Resolution by Crystallization Présentée et soutenue par Aliou MBODJI Thèse soutenue publiquement le 14 Mai 2020 devant le jury composé de M. Johan WOUTERS Professeur Université de Namur Rapporteur Mme. Jeanne CRASSOUS Directeur de Recherche Université de Rennes 1 Rapporteur Mme. Mihaela POP Docteur Entreprise TeraCrystal Examinateur Mme. Valérie DUPRAY MCF – HDR Université de Rouen Normandie Directeur de Thèse M. Gérard COQUEREL Professeur Université de Rouen Normandie Président M. Gabin GBABODE MCF Université de Rouen Normandie Membre invité M. Richard M KELLOGG Professeur Entreprise Syncom BV Membre invité Thèse dirigée par Valérie DUPRAY MCF-HDR et Co-encadrée par le Dr. Gabin GBABODE au laboratoire Sciences et Méthodes Séparatives (EA 3233 SMS) To my wife Boury, To my aunt Marianne, To my Family, To all my Friends, « L'intensité de ta foi augmente en fonction de la profondeur de tes pensées » Cheikh Ahmadou BAMB Acknowledgments First of all, I want to thank Professor Gérard Coquerel for allowing me to do my PhD thesis in his group: Science et Méthodes Séparatives (SMS laboratory) but also for making me discover lot of concepts on heterogeneous equilibria, preferential crystallization and more that had so far escaped me. I would like to thank you for the candidate compound you proposed to me for this work and for your daily take home wise lessons during our discussion. I am sure that they will bright my future carrier. I would like to take this opportunity to say a very big thank to my two supervisors, Dr Valérie Dupray and Dr Gabin Gbabode, for giving me the opportunity to achieve a so rewarding thesis, giving me the possibility to progress in the field of Material Chemistry and to discover a new speciality of chemistry: Crystallization. Both of you have shared with me knowledge on nonlinear optics, identification of critical crystallization parameters, solving crystal structure from crystals and powders etc. Discussing with both of you were immediately easy and your daily comments, suggestions and recommendations on my experimental results were always fruitful to pursue the work. You have inspired me for your humble and simplicity with great rigor. Specially, I would like to thank Dr Morgane Sanselme for helping to solve all the crystal structures. Without your collaboration, this work could not be achieved, I appreciate a lot your valuable work. I thank all the permanent members of the laboratory (Dr Clément Brandel, Dr Ivo Rietveld, Dr Nicolas Couvrat, Dr Yohann Cartigny, Prof. Samuel Petit, and Prof. Pascal Cardinael and colleagues of chromatography team) for the constructive discussions we have in their offices or during seminar. They were a source of motivation and thus give me courage to pursue this work and improve my results. Special thanks to Dr Simon Clevers and Dr Lina Yuan for their tutorials on SHG technique at the beginning of my PhD thesis. Thanks also to Dr Antoine Burel, Dr Bienvenu Atawa, Dr Clément De Saint Jores and Dr François Xavier Gendron for their help and support during their PhD period in the SMS laboratory. I thank all my colleagues: CORE members (Dr Ryusei Oketani and Lina Harfouche), Dr Manon Shindler, other PhD students (Kangli Li, Chloé Sainlaud, Laurérine Marc, Aurélien Lemercier, ~ 5 ~ Marine Hoquante and Mélody Briard), the members of the laboratory (Lucie Dautreaux, Celine Bensakoun and Marie Vaccaro) that allow daily to advance the science and all trainees who have crossed my path and helped to research and to the life of laboratory. I would like to thank Professor Richard M Kellogg, Dr Michel Leeman and Syncom BV, Groningen-The Netherlands, for providing me one of the compounds used for this work. Thanks a lot, to Prof. Kellogg and Dr Leeman for their valuable contribution to the publications of this work. During my thesis, I had the chance to spend one month in Nijmegen, The Netherlands, in the IMM laboratory, one month in Manchester, UK, in the CCAPPE laboratory, for my academic secondments and one month in Cluj-Napoca, Romania, TeraCrystal for my industrial secondment. I would like to thank respectively Professor Elias Vlieg and his group, Dr Thomas Vetter and his group, and Dr Mihaela Pop and his group which gave me the opportunity to discover more techniques and facilities for the characterization and chiral separation of organic compounds. I would like to thank the European Commission by funding this research through the CORE project (October 2016−September 2020) from the Horizon 2020 Research and Innovation Programme of the European Union under Marie Sklodowska-Curie Grant Agreement No. 722456 CORE ITN. This research and innovation programme gave me the opportunity to accomplish a PhD degree and to build a very important scientific network and to travel across Europe. Finally, I thank my mom Soukeye Dieng for all the love and support you have showed me, long life mommy and my dad Ibrahima who passed away in 2010. Special thanks to my aunt and mom Marianne Barry who passed away at the end of my PhD (beginning of 2020). I used to call you “Maman Barry”. For this auspicious occasion, I am indeed very grateful for all the love and support you have showed me since day one. You were my confident, my everything, you have done a lot for me, I will never forget to pray for you. Thanks to my other aunty Fambaye and other members of the family for their support always. Special thanks to my pretty wife Penda Boury Ndao Mbodji, my life. Your warm support is always with me, I love you, my heart. ~ 6 ~ TABLE OF CONTENTS TABLE OF CONTENTS ...................................................................................................................... 7 GENERAL INTRODUCTION .......................................................................................................... 12 DEFINITION OF SOME BASIC CONCEPTS USED IN THE MANUSCRIPT ......................... 14 CHAPTER 1: GENERALITIES ........................................................................................................ 16 PART 1 : THE CRYSTALLINE STATE ..................................................................................... 17 1.1. CRYSTALLINE STATE OF SOLIDS ............................................................................. 17 1.2. THE GROUP THEORY.................................................................................................... 18 1.2.1. Unit cell, crystal systems and Bravais lattices ................................................................. 18 1.2.2. Symmetry and symmetry operations ............................................................................... 19 1.2.3. Space groups .................................................................................................................... 21 1.3. STRUCTURAL CHARACTERIZATION OF CRYSTALLINE SOLIDS ...................... 22 1.3.2. X-ray powder diffraction (XRPD) ................................................................................... 23 1.3.3. Single Crystal X-Ray Diffraction (SC-XRD) .................................................................. 23 PART 2: THERMODYNAMICS AND HETEROGENEOUS EQUILIBRIA .......................... 25 2.1. CRYSTAL GENESIS ............................................................................................................ 25 2.1.1. Precipitation ..................................................................................................................... 25 2.1.1.1. Supersaturation ......................................................................................................... 25 2.1.2. Nucleation ....................................................................................................................... 25 2.1.2.1. Primary nucleation.................................................................................................... 25 2.1.2.2. Secondary nucleation................................................................................................ 27 2.1.3. Growth ............................................................................................................................. 27 2.2. HETEROGENEOUS EQUILIBRIA AND STABILITY ....................................................... 27 2.2.1. Phase equilibria ............................................................................................................... 27 2.2.2. Phase rule ........................................................................................................................ 28 2.2.3.