Academic literature on the topic 'Functional Gold Clusters'

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. 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 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 due to a compensation of errors. 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 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 towards an antibody. This process, known as ligand exchange reaction, is used to label proteins with gold clusters, as reducing agents cannot be used when certain biomolecules are present. Our results show that the neighbouring amino acids of the cysteine that should bind to the gold cluster play an essential role in the reaction. Finally, we focus on the study of the mechanism of the enzymatic reaction of a glycoprotein, a-1,3-glycosyltransferase. In recent years, our group has investigated the 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 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.<br>Los clústeres de oro protegidos por tiolatos (AuMPCs) se utilizan en varias aplicaciones biológicas y biomédicas debido a sus propiedades físicas y químicas. El hecho de que el enlace oro-azufre sea muy estable permite la unión de biomoléculas en la superficie de los clústeres de oro a través de una cisteína, un aminoácido que contiene un grupo tiol (SH). Sistemas específicos AuMPC-péptido pueden atravesar la barrera hematoencefálica sin alterar su integridad, pudiéndose utilizar para tratar patologías relacionadas con el sistema nervioso central, como el Alzheimer o el Parkinson. Además, los AuMPCs representan una alternativa a los biosensores tradicionales debido a sus propiedades ópticas y su especificidad ante ciertos antígenos cuando se escoge el sistema AuMPC-péptido adecuado. Métodos basados en la reducción de sales de oro han sido propuestos para sintetizar AuMPCs. En 1951 Turkevich y colaboradores usaron citrato sódico para la reducción de ácido cloroáurico. En 2002 un nuevo método sintético fue propuesto, denominado método de dispersión de átomos metálicos solvatados. En este método, átomos de oro neutros se mezclan con alcanotioles, resultando en la formación de AuMPCs e hidrógeno molecular. Este hecho, junto con la primera cristalización y determinación estructural de Au102(SR)44 llevada a cabo por Jadzinsky y colaboradores, desencadenó un gran debate en el campo, ya que los protones que inicialmente estaban presentes en los alcanotioles no se encontraron en la estructura cristalográfica. Uno de los objetivos de esta tesis es encontrar cómo los átomos de hidrógeno forman H2 durante la formación de AuMPCs. Con este fin, se utiliza metadinámica ab initio para descifrar el mecanismo molecular de la formación de AuMPCs partiendo de clústeres de oro neutros y alcanotioles (capítulo III). Clave para el uso de AuMPCs como biosensores es el conocimiento de sus propiedades ópticas. La energía HOMO-LUMO está relacionada con estas propiedades ópticas. La teoría del funcional de la densidad (DFT) ha sido muy utilizada para obtener valores teóricos de la energía HOMO-LUMO, aunque es sabido que subestima este valor con respecto al obtenido experimentalmente. Aún así, estudios computacionales recientes han seguido utilizando DFT para calcular valores de la energía HOMO-LUMO de AuMPCs, y sorprendentemente los valores obtenidos están de acuerdo con los resultados experimentales. Sin embargo, los sistemas estudiados siempre han sido modelos simplificados de los sistemas reales, originando la pregunta de si la coincidencia es fortuita debido a una compensación de errores. Nuestro objetivo es obtener valores de la energía HOMO-LUMO para sistemas utilizados experimentalmente, es decir, péptidos como ligandos y agua como disolvente (capítulo IV) para demostrar que únicamente un modelo realista y no sólo el uso de funcionales DFT adecuados puede dar resultados comparables con los experimentales. Como primer paso para entender la reactividad de AuMPCs frente a proteínas (capítulo V), se ha modelizado la unión de un AuMPC y un anticuerpo. Este proceso, conocido como reacción de intercambio de ligandos, se utiliza para marcar proteínas con clústeres de oro. Nuestros resultados muestran que los aminoácidos del entorno de la cisteína que debe unirse al clúster de oro juegan un papel esencial en la reacción. Finalmente nos centramos en el mecanismo enzimático de una glicoproteína, la a-1,3-glicosiltransferasa. Recientemente nuestro grupo ha investigado el mecanismo de una familia de glicosiltransferasas (GTs), obteniendo su itinerario catalítico. En esta tesis hemos extendido dicho estudio a otra familia de GTs para averiguar si existe un mecanismo común para todas las GTs. Este estudio representa un primer paso para la modelización de sistemas más complejos de GTs inmovilizadas por AuMPCs, una técnica prometedora para el desarrollo de glicosíntesis automatizada. Los métodos teóricos utilizados en la tesis se describen en el capítulo II.

In this work the electronic and structural properties of anatase TiO2 (100) surface and gold adsorption have been investigated by using the first-principles calculations based on density functional theory (DFT). TiO2 is a wide band-gap material and to this effects it finds numerous applications in technology such as, cleaning of water, self-cleaning, coating, solar cells and so on. Primarily, the relation between the surface energy of the anatase (100)-1x1 phase and the TiO2-layers is examined. After an appropriate atomic layer has been chosen according to the stationary state of the TiO2 slab, the adsorption behavior of the Au atom and in the different combinations are searched for both the surface and the surface which is supported by a single Au atom/atoms. It has been observed that a single Au atom tends to adsorb to the surface which has an impurity of Au atom or atoms. Although, the high metal concentration on the surface have increased the strength of the adsorption, it is indicated that the system gains a metallic property which is believed to cause problems in the applications. In addition, the gold clusters of the dimer (Au2) and the trimer (Au3) have been adsorbed on the surface and their behavior on the surface is investigate. It is observed that the interaction between Au atoms in the atomic cluster each other is stronger than that of gold clusters and the surface.

Research Doctorate - Doctor of Philosophy (PhD)<br>The absorption cross-section over the optical range of frequencies of gold and silver clusters of up to 171 atoms was calculated using time-dependent density functional theory. Calculations were performed using the package Octopus and used the explicit time propagation method. The wavefunctions were calculated over a real-space grid and exchange-correlation interactions were including using the local density approximation. Structures were cleaved from a bulk crystal and included high-symmetry structures as well as structures with lower levels of symmetry. The evolution of the absorption spectra over cluster size was investigated and several trends were identified. As cluster size increases the absorption spectra becomes smoother. For gold clusters with more than approximately 70 atoms, the absorption spectra have several common features, including an absorption peak at around 2.5-3.0 eV, commonly attributed to a plasmonic oscillation. Absorption spectra were compared to past calculations and experimental measurements where available. For gold clusters above approximately 150 atoms, the calculated absorption spectra are in reasonable agreement with Mie theory calculations and experimental measurements. The effect of different calculation methods and approximations on the calculated absorption cross-section was also identified. The inclusion of spin-polarisation and the use of an exchange-correlation potential using the generalised gradient approximation had minor impact on the calculated absorption spectra. A new method of analysing the nature of peaks in the absorption spectra was also investigated. This method entailed exciting the system at a single frequency, and analysing the evolution of the electron density over time. This initial investigation indicated a difference in the evolution of the system when it was oscillated at a frequency corresponding to a plasmonic response as compared to a frequency corresponding to an electron hole excitation. This possibly indicates a method for investigating the nature of a plasmonic response in clusters of this size. This thesis demonstrates that with current computing power the optical absorption spectra of metallic clusters can be calculated using time-dependent density functional theory over a continuous range of cluster sizes from several atoms up almost to the point at which classical calculations become accurate. It identifies what calculation parameters are important to the optical absorption spectra for future calculations to agree with classical calculations as more computing power becomes available.

The formation and patterns of a monolayer are determined by the interplay of two fundamental interactions, adsorbate-substrate and intermolecular interactions. The binding strength between adsorbate and substrate affects the mobility of the adsorbate at the surface and the stability of the complex. The intermolecular interaction plays a significant role in the monolayer patterns on the epitaxial layer of the substrate. A monolayer can be formed either by a spontaneous self-assembly, or by fabrication via atomic-layer deposition (ALD). The physical and chemical properties of the resulting monolayer have a broad array of applications in fabricating functional materials for hydrophobic or hydrophilic surfaces, biological sensors, alternating the properties of the substrate, catalysis and forming ordered layered structures. In this dissertation, the investigation focuses primarily on the influence of the surface topology on the binding behaviour of adsorbate-surface complexes. The state of the art DFT-TS method is used to simulate the sulfur-containing amino acids at complex gold surfaces and examine the relationship between the binding strengths and the binding sites with various nearest neighbouring environments. The same method is also used to determine if a chemical reaction will take place for various catalytic silicon precursors at a silicon oxide surface. Simulating surface chemistry using the DFT-TS method requires intensive com- puting resources, including CPU use and computing time. Another focus of this dissertation is to increase the data generating speed by reducing the size of the sim- ulated systems without altering the outcome. A relatively small gold cluster is used to study the binding behaviours of small organic molecules on the cluster. The same strategy is also used to simulate the chemical reactions between various self-catalying silicon precursors and a water molecule.<br>Graduate<br>2021-10-21

Transition metal alloys are an important class of materials in heterogeneous catalysis due in no small part to the often greatly enhanced activity and selectivity they exhibit compared to their monometallic constituents. A host of experimental and theoretical studies have demonstrated that, in many cases, these synergistic effects can be attributed to atomic-scale features of the catalyst surface. Realizing the goal of designing -- rather than serendipitously discovering -- new alloy catalysts thus depends on our ability to predict their atomic configuration under technologically relevant conditions. This dissertation presents original research into the development and use of computational tools to accomplish this objective. These tools are all based on a similar strategy: For each of the alloy systems examined, cluster expansion (CE) Hamiltonians were constructed from the results of density functional theory (DFT) calculations, and then used in Metropolis Monte Carlo (MC) simulations to predict properties of interest. Following a detailed description of the DFT+CE+MC simulation scheme, results for the AuPd/Pd(111) and AuPt/Pt(111) surface alloys are presented. These two systems exhibit considerably different trends in their atomic arrangement, which are explicable in terms of their interatomic interactions. In AuPd, a preference for heteronuclear, Au-Pd interactions results in the preferential formation of Pd monomers and other small ensembles, while in AuPt, a preference for homonuclear interactions results in the opposite. AuPd/Pd(100) and AuPt/Pt(100) were similarly examined, revealing not only the effects of the same heteronuclear/homonuclear preferences in this facet, but also a propensity for the formation of second nearest-neighbor pairs of Pd monomers, in close agreement with experiment. Subsequent simulations of the AuPd/Pd(100) surface suggest the application of biaxial compressive strain as a means increasing the population of this catalytically important ensemble of atoms. A method to incorporate the effects of subsurface atomic configuration is also presented, using AuPd as an example. This method represents several improvements over others previously reported in the literature, especially in terms of its simplicity. Finally, we introduce the dimensionless scaled pair interaction, whereby the finite-temperature atomic configuration of any bimetallic surface alloy may be predicted from a small number of relatively inexpensive calculations.<br>text