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Ab Initio Molecular Dynamics Study of Thiolate-Protected Gold Clusters and Their

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Ab Initio Molecular Dynamics Study of Thiolate-Protected Gold Clusters and Their UNIVERSITAT POLITÈCNICA DE CATALUNYA FACULTAT DE FÍSICA, DEPARTAMENT DE FÍSICA APLICADA PROGRAMA DE DOCTORAT DE FÍSICA COMPUTACIONAL I APLICADA AB INITIO MOLECULAR DYNAMICS STUDY OF THIOLATE-PROTECTED GOLD CLUSTERS AND THEIR INTERACTION WITH BIOMOLECULES Tesi presentada per obtenir el títol de Doctor per la Universitat Politècnica de Catalunya per part d’en Víctor Rojas-Cervellera realitzada al Parc Científic de Barcelona i al Departament de Química Orgànica de la Facultat de Química de la Universitat de Barcelona, sota la direcció de la Dra. Carme Rovira Virgili Professora d’Investigació ICREA, i comptant amb la tutoria de la Dra. Elvira Guàrdia Manuel Professora del Departament de Física i Enginyeria Nuclear de la Universitat Politècnica de Catalunya. Barcelona, Juny 2015 ii Abstract Thiolate monolayer-protected gold clusters (AuMPCs) have been attracted much interest in the last years. The fact that AuMPCs can form conjugates with biomolecules allow scientist to use them as carriers of chemotherapeutic drugs, with promising applications in a broad range of diseases, including cancer and neurodegenerative diseases. However, little is known on the molecular mechanism leading to formation of AuMPCs and its reactivity towards proteins. In this thesis, we use ab initio molecular dynamics simulations to unravel the mechanism of formation of AuMPCs from a neutral gold cluster and thiol molecules. Afterwards, we uncover the mechanism of the ligand-exchange reaction of a peptide-protected AuMPC with an antibody. Finally, we model the enzymatic reaction of an enzyme responsible for the synthesis of oligosaccharides, α-1,3-glycosyltransferase, as a first step to study the glycosyl transfer reaction on more complex sugar-protected gold nanoparticle systems. A better understanding of the enzymatic mechanism will help the rational design of inhibitors in order to treat diseases where glycosyltransferases are important. Keywords: thiolate monolayer-protected gold clusters, staple motif, glycosyltransferases, carbohydrates, ab initio molecular dynamics, density functional theory, Car-Parrinello molecular dynamics, metadynamics, HOMO-LUMO gap. iii Preface Thiolate monolayer-protected gold clusters (AuMPCs) are being used in various biological and biomedical applications due to their unique physical and chemical properties. The fact that gold-sulphur bonds are very stable enables the binding of biomolecules in the surface of gold clusters through a cysteine, an amino acid that contains a thiol group (SH). Specific AuMPCs-peptide conjugates can cross the blood- brain barrier without altering its integrity, opening the door for the treatment of pathologies related to the central nervous system, such as Alzheimer or Parkinson. Moreover, AuMPCs represent an alternative to the traditional fluorescence-based biosensors, due to their optical properties and its ability to bind specific antigens when certain AuMPCs-antibody conjugates are used. A brief introduction of these biological and biomedical applications can be found in Chapter I, as well as a description of the main synthetic methods of AuMPCs and an analysis of the AuMPC’s structures. Several synthetic approaches based on the reduction of gold salts have been proposed to synthesize AuMPCs. In 1951 Turkevich and co-workers used sodium citrate for the reduction of chloroauric acid. In 2002 a novel synthetic method was proposed, named solvated metal atom dispersion method. In this method, neutral gold atoms were mixed with alkanethiols, resulting in the formation of AuMPCs, and molecular hydrogen was detected. This finding, together with the first crystallization and X-ray structure determination of Au102(SR)44 by Jadzinsky et.al., triggered a debate in the field, since the protons that were initially present in alkanethiols were not found in the AuMPC structure. One of the main goals of the present thesis is to elucidate where the alkanethiol hydrogens go during the formation of the AuMPC. To this aim, ab initio metadynamics have been used to unravel the molecular mechanism of the formation of AuMPCs departing from neutral gold clusters and alkanethiols (Chapter III). Key to the usage of AuMPCs as biosensors is the better knowledge of their optical properties. The energetic difference between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), i.e. the HOMO- LUMO gap, is a physical parameter related with optical properties. Density Functional Theory (DFT) is extensively used to obtain a theoretical value of the HOMO-LUMO gap, although it is known to severely underestimate it with respect to the experimental values. Nevertheless, recent computational studies using DFT have reported values of the HOMO-LUMO gap of AuMPCs in a very close agreement with the experimental ones. However, a simplified model of the real system was used, raising the question whether the agreement between the theoretical and the experimental values is fortuitous. Our goal is to obtain HOMO-LUMO gap values using the whole experimental systems, i.e. peptides as the protecting ligands of the gold core and iv water as solvent (Chapter IV) to demonstrate that only a realistic model, and not only the use of appropriate DFT functionals, can lead to values comparable to the experimental ones. In a first step for the understanding of the reactivity of AuMPCs towards proteins, in Chapter V we modelled the binding of AuMPC to the N-terminal end of the anti-influenza N9 neuraminidase NC10 antibody. This process, known as ligand exchange reaction, is used to label proteins with gold clusters, since reducing agents cannot be used with certain biomolecules. Our results show that the neighbouring amino acids of the cysteine that binds to the gold cluster play an essential role in the ligand exchange reaction. Finally, we investigated the mechanism of the enzymatic reaction of a glycoprotein, α-1,3-glycosyltransferase. In recent years, our group has investigated the molecular mechanism of one family of glycosyltransferases (GTs), providing its catalytic itinerary. In this thesis we extend this study to another family of GTs to elucidate whether or not a common molecular mechanism operates for GTs. This study represents one step towards the modelling of the more complex glycosyl transfer reaction on glycosyltransferases immobilized by gold nanoparticles, a promising technique for the development of automated glycosynthesis. The theoretical methods used along this thesis are detailed in Chapter II. v Acknowledgments Aquesta tesi no hauria estat possible sense l’ajuda de tota la gent que ha estat al meu costat durant aquests anys. Voldria agrair de manera especial: A la Carme, per la seva confiança i els seus consells. Gràcies per la teva dedicació i per tot el que m’has arribat a ensenyar durant aquests anys. Sempre t’estaré agraït. I would also thank to Jaakko the opportunity he gave me to visit his group in Tampere, Finland. Thanks for the great scientific ideas that you had. This thesis is in part thanks to you. A tota la gent del laboratori: al Fermín, que em va introduir en el món de la Química Computacional quan encara estava acabant la carrera. A l’Albert, per tenir tanta paciència amb mi. He après moltíssimes coses de tu. Xevi, Pietro, Marc M., Javier, Oriol, Marc W., Santi, Alba,... guardo molt bon record de tots vosaltres, sobretot de totes les tertúlies a la hora del cafè. Sogol: you are the best English teacher of the world. Morageb bash. Javi: amb tu he compartit tots els anys de tesi; ets un gran doctor, un gran company i un gran amic. Ens queden moltes maratons per córrer junts! Mertxe: gràcies per ser tan bona mestra. Lluís: He intentat ensenyar-te tot el que he pogut, però no se qui ha après més de qui. A mi grupo de amigos: Javi, Jonathan, Nacho, Oriol, Raúl, Samuel y Soto. Sin duda, sois parte de esto. A toda mi familia, pero en especial a mis padres, que siempre han confiado en mí. Gracias por ayudarme en todo momento, vuestro apoyo ha sido esencial. A l’Ariadna: amb tu he compartit moltes coses durant aquests anys, que al teu costat han estat inoblidables. Moltes gràcies per ajudar-me dia a dia, ets la millor companya que es pot tenir. Aquesta tesi al teu costat ha estat molt més fàcil. vi Table of Contents Abstract .................................................................................................................. iii Preface .................................................................................................................... iv Acknowledgements ................................................................................................. vi List of Abbreviations and Symbols ............................................................................ x Chapter I - Introduction ............................................................................................ 1 Thiolate Monolayer-Protected Gold Clusters ................................................................ 3 Historical Overview .................................................................................................... 3 Synthesis of Monolayer-Protected Gold Clusters and Nanoparticles ....................... 4 Structure of Thiolate Monolayer-Protected Gold Clusters and Nanoparticles ......... 5 Biological Applications of AuMPCs and AuMPNs ....................................................... 9 Glycosyltransferases (GTs) ........................................................................................... 11 Carbohydrates .........................................................................................................
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