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Molecular Quantum Similarity in Qsar: Applications in Computer-Aided Molecular Design

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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. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art. 32 del Texto Refundido de la Ley de Propiedad Intelectual (RDL 1/1996). Para otros usos se requiere la autorización previa y expresa de la persona autora. En cualquier caso, en la utilización de sus contenidos se deberá indicar de forma clara el nombre y apellidos de la persona autora y el título de la tesis doctoral. No se autoriza su reproducción u otras formas de explotación efectuadas con fines lucrativos ni su comunicación pública desde un sitio ajeno al servicio TDR. Tampoco se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR (framing). Esta reserva de derechos afecta tanto al contenido de la tesis como a sus resúmenes e índices. WARNING. Access to the contents of this doctoral thesis and its use must respect the rights of the author. It can be used for reference or private study, as well as research and learning activities or materials in the terms established by the 32nd article of the Spanish Consolidated Copyright Act (RDL 1/1996). Express and previous authorization of the author is required for any other uses. In any case, when using its content, full name of the author and title of the thesis must be clearly indicated. Reproduction or other forms of for profit use or public communication from outside TDX service is not allowed. Presentation of its content in a window or frame external to TDX (framing) is not authorized either. These rights affect both the content of the thesis and its abstracts and indexes. 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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