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Molecular Quantum Similarity in Qsar: Applications in Computer-Aided Molecular Design MOLECULAR QUANTUM SIMILARITY IN QSAR: APPLICATIONS IN COMPUTER-AIDED MOLECULAR DESIGN Ana GALLEGOS SALINER ISBN: 84-689-0623-9 Dipòsit legal: GI-1168-2004 http://hdl.handle.net/10803/7937 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. 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Doctoral Thesis for the obtaining of the degree of Doctor in Theoretical and Computational Chemistry MOLECULAR QUANTUM SIMILARITY IN QSAR: APPLICATIONS IN COMPUTER-AIDED MOLECULAR DESIGN Ana Gallegos Saliner Girona, June 2004 Institut de Química Computacional Departament de Química Universitat de Girona El sotasignat, Professor Ramon Carbó-Dorca i Carré, Catedràtic d’Universitat del Departament de Química de la Universitat de Girona CERTIFICA: Que Ana Gallegos i Saliner, llicenciada en Química per la Universitat de Girona, ha realitzat sota la meva direcció, a l’Institut de Química Computacional i al Departament de Química de la Universitat de Girona, el treball d’investigació titulat: “Molecular Quantum Similarity in QSAR: Applications in Computer-Aided Molecular Design” que es recull en aquesta memòria i es presenta en pública defensa per a optar al grau de Doctora en Química Teòrica i Computacional. I, perquè consti als efectes legals escaients, signo aquest certificat a Girona, el 20 d’Abril de 2004. Ramon Carbó-Dorca Director de l’Institut de Química Computacional Professor Catedràtic de la Universitat de Girona Girona, 20 d’Abril de 2004 A la meva família, A les meves amigues de Figueres, Als de Castelló, Als companys i amics IQC, Per tots vosaltres! Ara mateix enfilo aquesta agulla amb el fil d'un propòsit que no dic i em poso a apedaçar. Cap dels prodigis que anunciaven taumaturgs insignes no s'ha complert i els anys passen de pressa. De res a poc, i sempre amb vent de cara, quin llarg camí d'angoixa i de silencis. I som on som; més val saber-ho i dir-ho i assentar els peus en terra i proclamar-nos hereus d'un temps de dubtes i renúncies en què els sorolls ofeguen les paraules i amb molts miralls mig estrafem la vida. De res no ens val l'enyor o la complanta, ni el toc de displicent malenconia que ens posem per jersei o per corbata quan sortim al carrer. Tenim a penes el que tenim i prou: l'espai d'història concreta que ens pertoca i un minúscul territori per viure-la. Posem-nos dempeus altra vegada i que se senti la veu de tots, solemnement i clara. Cridem qui som i que tothom ho escolti. I, en acabat, que cadascú es vesteixi com bonament li plagui, i via fora, que tot està per fer i tot és possible. Ara mateix Miquel Martí i pol MOLECULAR QUANTUM SIMILARITY IN QSAR: APPLICATIONS IN COMPUTER-AIDED MOLECULAR DESIGN Ana Gallegos Saliner Contents Contents Preface........................................................................................................................................... i 1 Presentation...................................................................................................................... v 2 Structure of the memory.................................................................................................. vi 3 Acknowledgements.......................................................................................................viii Introduction................................................................................................................................. 1 1 General Introduction........................................................................................................ 5 1.1 Molecular Quantum Similarity (MQS).................................................................... 7 1.2 Quantitative Structure-Activity Relationships (QSAR) .......................................... 8 1.3 Molecular Similarity in QSAR................................................................................ 9 2 Overview........................................................................................................................ 11 References............................................................................................................................... 15 Quantum Similarity Theory..................................................................................................... 23 1 Introduction.................................................................................................................... 27 2 Introduction to Similarity............................................................................................... 31 2.1 The concept of similarity....................................................................................... 31 2.2 Molecular Quantum Similarity.............................................................................. 32 3 Quantum mechanics and the role of Density Function .................................................. 35 3.1 The Wavefunction: First postulate of Quantum Mechanics.................................. 35 3.2 Born’s interpretation: Probability distribution Density Function.......................... 35 3.3 Experimentally measurable properties: Fifth postulate of Quantum Mechanics... 37 3.4 Density Function construction............................................................................... 38 3.4.1 First-order Density Function............................................................................. 39 3.4.2 Ab initio Density Function................................................................................ 40 3.4.3 Density Function of a molecular fragment........................................................ 42 3.5 Fitted Density Function ......................................................................................... 42 3.5.1 Atomic Shell Approximation (ASA) ................................................................ 44 3.5.2 Promolecular Atomic Shell Approximation (PASA)........................................ 46 3.5.3 ASA adjustment method ................................................................................... 49 4 Molecular Quantum similarity Measures (MQSM) ....................................................... 52 4.1 General Definition of MQSM ............................................................................... 52 4.2 Types of Molecular Quantum Similarity Measures .............................................. 54 4.2.1 Overlap QSM .................................................................................................... 54 4.2.2 Coulomb QSM .................................................................................................. 55 4.2.3 Kinetic Energy QSM......................................................................................... 55 4.2.4 Molecular Quantum Self-SM............................................................................ 56 Contents 4.2.5 Fragment Quantum Self-SM............................................................................. 56 4.2.6 Triple-density QSM.........................................................................................
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