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Approches Structure-Propriété Pour La Prédiction Des Propriétés Physico-Chimiques Des Substances Chimiques

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Approches Structure-Propriété Pour La Prédiction Des Propriétés Physico-Chimiques Des Substances Chimiques THÈSE DE DOCTORAT DE L’UNIVERSITÉ PIERRE ET MARIE CURIE Présentée le 25 septembre 2013 par Vinca Prana Pour obtenir le grade de DOCTEUR de l’UNIVERSITÉ PIERRE ET MARIE CURIE École Doctorale Chimie Physique et Analytique de Paris VI Spécialité Chimie théorique et informatique Approches structure-propriété pour la prédiction des propriétés physico-chimiques des substances chimiques devant le jury composé de : Pr. Henry Chermette Rapporteur Pr. Alexandre Varnek Rapporteur Pr. Esmaïl Alikhani Examinateur Dr. David André Examinateur Dr. Guillaume Fayet Examinateur Dr. Patricia Rotureau Encadrante INERIS Pr. Carlo Adamo Directeur de thèse "There are three kinds of lies: lies, damned lies, and statistics." Mark Twain - Chapters from My Autobiography REMERCIEMENTS Je voudrais tout d’abord remercier mon directeur de thèse, M. Carlo Adamo de m’avoir donné l’occasion de travailler dans son équipe de Modélisation des Systèmes Complexes de Chimie ParisTech où il encourage l’esprit de convivialité ainsi que pour la confiance qu’il m’a accordée. J'adresse aussi mes remerciements à ma co-encadrantre de thèse INERIS, Mme Patricia Rotureau, ainsi qu’à M. Guillaume Fayet pour avoir supervisé mon travail. Je tiens également à remercier Messieurs Henry Chermette et Alexandre Varnek d’avoir accepté d’être les rapporteurs de ce manuscrit ainsi qu’aux examinateurs Messieurs Esmaïl Alikhani et David André d’avoir accepté de faire partie de mon jury de thèse. Je remercie Ilaria pour ses conseils et ses recommandations, notamment pour l’avenir. Merci à l’ensemble de l’équipe du MSC avec qui j’ai passé de bons moments : Fred (le spécialiste crystal aussi chef des TD), Diane pour les discussions de la pause thé/infusion, Romain, Bertrand et tous ceux qui ont fait des passages plus ou moins longs dans l’équipe. Mais je remercie aussi ceux qui, devenus docteurs, sont parti vers de nouveaux horizons : Cyril, Tangui, Aurélien pour les discussions de fin de journée, Giuseppe, Éric pour son initiation au python et sa bonne humeur quotidienne, Amel pour sa gentillesse (et ses délicieux gâteaux !) et Nils pour ses conseils littéraires et son aide. Je n’ai pas oublié celles avec qui j’ai eu la chance de profiter du bon air de Verneuil et de partager les trajets Paris-Creil. Un grand merci à Stefania pour son aide à mes débuts et ses bons conseils en termes de séries et Stefanina pour les « sessions zumba® » et les soirées pizza. Mes remerciements vont aussi à mes parents, Elisa et Yohan pour m’avoir soutenu, chacun à sa manière, ainsi que pour leur patience aux cours de ces années dont le nombre dépasse (largement) trois. SOMMAIRE Remerciements ........................................................................................................................................5 Liste des acronymes .............................................................................................................................. 11 Chapitre 1 : contexte et objectifs .......................................................................................................... 15 I. Réglementations Européennes des substances chimiques .............................................. 17 1. Le règlement REACH .............................................................................................................. 17 2. Les procédures de REACH...................................................................................................... 18 3. Règlements associés : CLP et TMD ........................................................................................ 20 4. Méthodes alternatives .......................................................................................................... 23 II. PREDIMOL ......................................................................................................................... 24 III. Les peroxydes organiques ................................................................................................. 26 1. Définitions et propriétés ....................................................................................................... 26 2. Caractérisation ...................................................................................................................... 28 3. Classification des peroxydes organiques ............................................................................... 29 4. Accidentologie liées aux peroxydes organiques ................................................................... 31 5. Sécurité .................................................................................................................................. 32 IV. Plan du manuscrit de thèse .............................................................................................. 35 V. Références ........................................................................................................................ 36 Chapitre 2 –De l’atome à la molécule : rappels de théorie ................................................................... 41 I. De l’équation de Schrödinger à Hartree-Fock .................................................................. 43 1. L’équation de Schrödinger .................................................................................................... 43 2. Born-Oppenheimer ............................................................................................................... 43 3. Approximation orbitalaire ..................................................................................................... 44 4. Equations de Hartree-Fock .................................................................................................... 45 5. Fonctions de bases ................................................................................................................ 46 II. Au-delà de Hartree-Fock ................................................................................................... 47 1. Théorie de la fonctionnelle de la densité .............................................................................. 47 2. DFT conceptuelle ................................................................................................................... 51 III. Mécanique moléculaire .................................................................................................... 52 1. Paramétrisation des champs de forces ................................................................................. 54 2. Limites de la méthode ........................................................................................................... 54 IV. Analyse conformationnelle ............................................................................................... 55 1. Principe et fonctionnement .................................................................................................. 55 2. Validation du programme ..................................................................................................... 58 V. Conclusion ......................................................................................................................... 61 VI. Références ........................................................................................................................ 62 Chapitre 3 - Principe et méthodes des modèles QSPR .......................................................................... 65 I. Principe ............................................................................................................................. 67 II. Base de données ............................................................................................................... 68 III. Représentation des structures.......................................................................................... 69 IV. Descripteurs ...................................................................................................................... 70 1. Définition ............................................................................................................................... 70 2. Classement par type .............................................................................................................. 70 3. Sélection des descripteurs ..................................................................................................... 71 V. Développement de modèles ............................................................................................. 73 1. Jeux d’entraînement et de validation ................................................................................... 73 2. Méthodes d’entraînement des données ............................................................................... 76 3. Mesure de l’ajustement ........................................................................................................ 77 VI. Validation .......................................................................................................................... 78 1. Validation croisée .................................................................................................................. 78 2. Corrélation par chance : Y-scrambling .................................................................................. 80 3. Validation externe ou prédictivité ......................................................................................... 81 4. Critères de validation ............................................................................................................ 83 VII. Domaine d’applicabilité
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