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Katarzyna M. ROMEK Katarzyna M. ROMEK Mémoire présenté en vue de l’obtention du grade de Docteur de l'Université de Nantes sous le sceau de l’Université Bretagne Loire grade de Docteur de Lodz University of Technology École doctorale : « 3MPL Matière, Molécules, Matériaux en Pays de la Loire » Discipline : Chimie Spécialité : Chimie analytique Unité de recherche : CEISAM; Université de Nantes Unité de recherche : Institute of Applied Radiation Chemistry ; Lodz University of Technology Soutenue le 09 Decembre 2016 Thèse N° : Studies of isotopic fractionation of 13C during biosynthesis and enzymatic reactions JURY Président : Gérald REMAUD, Professeur, Université de Nantes Rapporteurs : Jaleh GHASHGAIE, Professeur, Université de Paris XI Roland WERNER, Ingénieur de Recherche, ETH Zurich Examinateurs : Michael DE WAARD, Directeur de Recherche, Université de Nantes Agnieszka DYBAŁA-DEFRATYKA, Dr. hab, Lodz University of Technology Małgorzata SZYNKOWSKA, Proffeseur, Lodz University of Technology Beata KOLESIŃSKA, Dr. hab, Lodz University of Technology Directeur de Thèse : Richard ROBINS, Directeur de Recherche, Université de Nantes Co-Directeur de Thèse : Piotr PANETH, Proffeseur, Lodz University of Technology Co-encadrant de Thèse : Pierrick NUN, Maître de Conférences, Université de Nantes Acknowledgments This work has been carried out in two teams – the EBSI (Elucidation of Biosynthesis by Iso‐ topic Spectrometries) group of the CEISAM (Chemistry and Interdisciplinarity: Synthesis, Analysis and Modelling) laboratory (University of Nantes, France) and the LIES (Laboratory of Isotope Effects Stud‐ ies) group in the Chemistry Department (Lodz University of Technology, Poland). I thank the French embassy in Warsaw for a Bursary from the French Government that par‐ tially financed this thesis studies. I would like to warmly thank my supervisor Dr Richard J. Robins, first for his patience and an ocean of support through all the years that I have had the pleasure to work with him, secondly for his substantive and moral feedback at every level and last but not least for his great sense of humour and belief in me. I would like to express my appreciation to my supervisor Prof Piotr Paneth for giving me the opportunity of working on the computational chemistry field and broaden my horizons. I would also thank to my co‐supervisor Dr Pierrick Nun for being there when the chemistry get complicated. A huge thank‐you goes to Virginie Silvestre, who spent numerous hours on giving me training on irm13C‐NMR and her valuable advices. Also to Benoit Charrier for making sure that I knew how not to break the spectrometers! I would like to thank to Prof Gérald Remaud for his precious comments on my work and his help with interpretation of the results, as well as to Serge Akoka, who made NMR understandable. For keeping irm‐EA/MS measurements enjoyable I want to thank Mathilde Grand, Anne‐ Marie Schiphorst and Ingrid Antheaume. Great thanks to Denis Loquet for help with the GC and HPLC analyses. To the EBSI team (whose composition was changing within the time) – thank you for your constant support through all the years and putting up with my temper. Special thanks to Dr Maxime Julien who always had time for discussion, either scientific or not, and never refused his help. To Dr MBaye Diaw Dioum who, on rainy days always managed to bring a smile with him and cheer me up. To Dr Rémi Vanel for finding solutions when thought that the light at the end of the tunnel had al‐ ready gone. To Laetitia Rouger for her kindness and feminine touch in the team. To Boris Gouilleux for having ‘sharp’ jokes exchange. To Valentin Joubert for the peaceful atmosphere at the office when it was needed and great Saturday nights parties. To Tangi Jezequel for coping with my bad temper. I would like to thank to Dr Kathy Chen who was always having good and positive vibrations that kept me in a positive thinking mode, especially during the past few months before my defence. To the LIES team – thank you for taking me under your theoreticians’ wings and making the impossible – possible. Special thanks to Agnieszka Krzemińska‐Kowalska without whom theoretical calculations will still be in the area of the dark arts, who spent numerous days on explanations and was the best companion for life outside the laboratory. To Dr Agnieszka Dybała‐Defratyka for her comments and support. To Dr Anna Grzybkowska who always had the time to help me along. For her huge support (day and night) I would like to thank Roxana Vasilescu, who always knew how and when to scold me over a few glasses at Chateaulain Wednesdays. 2 The list of people who were standing by my side and to whom I am very grateful for their presence is possibly longer than this dissertation, so I would like to say thank you to all the members of CEISAM laboratory for making this place friendly, safe and almost like home. I would also like to thank to all of the people who never had anything to do with chemistry and they still are my friends and whom support I felt through thick and thin. Last but not least I want to thank my entire family for their constant support, optimism and enormous dose of patience during my thesis. For keeping me calm and sane as well as supporting me on my way I want to thank to An‐ toine Mazel. 3 Table of contents Acknowledgments ............................................................................................................................ 2 Terms and Definitions .................................................................................................................... 10 Abbreviations ................................................................................................................................. 11 1 Chapter I ‐ Objectives of the Study and Summary of the Results .......................................... 13 1.1 Objectives ....................................................................................................................... 13 1.2 Methods ......................................................................................................................... 13 1.3 Results ............................................................................................................................ 13 1.4 Conclusions .................................................................................................................... 14 2 Chapter II ‐ Introduction ......................................................................................................... 15 2.1 Isotopic fractionation in natural products ..................................................................... 15 2.1.1 Definition and occurrence of isotopes ....................................................................... 15 2.1.2 Definition and causes of isotopic fractionation ......................................................... 15 2.1.3 Expressing Isotopic fractionation ............................................................................... 19 2.1.4 Fractionation associated with primary carbon fixation ............................................. 22 2.1.4.1 Fractionation effects due to diffusion ................................................................ 22 2.1.4.2 Fractionation in terrestrial C3 plants .................................................................. 23 2.1.4.3 Fractionation in C4 plants ................................................................................... 23 2.1.4.4 Fractionation in Crassulacean acid metabolism plants ...................................... 24 2.1.5 Fractionation in carbon associated with post‐photosynthetic metabolism .............. 25 2.1.6 How the fractionation is happening: thermodynamic considerations ...................... 29 2.1.7 Exploitation of isotopic fractionation to probe enzyme mechanisms ....................... 30 2.2 Methods of measurements ............................................................................................ 33 2.2.1 Isotope ratio monitoring by MS ................................................................................. 33 2.2.1.1 Overall scheme of the machine and protocol of measurements ...................... 33 2.2.2 Isotope ratio monitoring by 13C NMR ........................................................................ 37 2.2.2.1 General aspects of NMR spectroscopy .............................................................. 37 2.2.2.2 Specific aspects of NMR spectrometry applied to isotope ratio monitoring .... 37 4 2.2.2.2.1 1H decoupling ............................................................................................... 38 2.2.2.2.2 Sample preparation ...................................................................................... 40 2.2.2.2.3 Intrinsic NMR properties of the target molecule ......................................... 41 2.2.2.2.4 Spectral treatment ....................................................................................... 42 3 Chapter III – Isotope distribution in amino acids .................................................................... 43 3.1 Amino acids ‐ overview .................................................................................................. 43 3.1.1 Amino acid pathways and classification ..................................................................... 43 3.1.2 Prior studies of isotopic fractionation in amino acids ................................................ 45 3.1.2.1 Global values .....................................................................................................
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