Yes / We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.

Yes / Peptide-mediated synthesis and assembly of nanostructures opens new routes to functional inorganic/organic hybrid materials. However, understanding of the many factors that influence the interaction of biomolecules, specifically peptides, with metal surfaces remains limited. Understanding of the relationship between peptide sequence and resulting binding affinity and configurations would allow predictive design of peptides to achieve desired peptide/metal interface characteristics. Here, we measured the kinetics and thermodynamics of binding on a Au surface for a series of peptide sequences designed to probe specific sequence and context effects. For example, context effects were explored by making the same mutation at different positions in the peptide and by rearranging the peptide sequence without changing the amino acid content. The degree of peptide-surface contact, predicted from advanced molecular simulations of the surface-adsorbed structures, was consistent with the measured binding constants. In simulations, the ensemble of peptide backbone conformations showed little change with point mutations of the anchor residues that dominate interaction with the surface. Peptide-capped Au nanoparticles were produced using each sequence. Comparison of simulations with nanoparticle synthesis results revealed a correlation between the colloidal stability of the Au nanoparticles and the degree of structural disorder in the surface-adsorbed peptide structures for this family of sequences. These findings suggest new directions in the optimization and design of biomolecules for in situ peptide-based nanoparticle growth, binding, and dispersion in aqueous media.

Yes / The adsorption of three homo-tripeptides, HHH, YYY, and SSS, at the aqueous Au interface is investigated, using molecular dynamics simulations. We find that consideration of surface facet effects, relevant to experimental conditions, opens up new questions regarding interpretations of current experimental findings. Our well-tempered metadynamics simulations predict the rank ordering of the tripeptide binding affinities at aqueous Au(111) to be YYY > HHH > SSS. This ranking differs with that obtained from existing experimental data which used surface-immobilized Au nanoparticles as the target substrate. The influence of Au facet on these experimental findings is then considered, via our binding strength predictions of the relevant amino acids at aqueous Au(111) and Au(100)(1 × 1). The Au(111) interface supports an amino acid ranking of Tyr > HisA ≃ HisH > Ser, matching that of the tripeptides on Au(111), while the ranking on Au(100) is HisA > Ser ≃ Tyr ≃ HisH, with only HisA showing non-negligible binding. The substantial reduction in Tyr amino acid affinity for Au(100) vs Au(111) offers one possible explanation for the experimentally observed weaker adsorption of YYY on the nanoparticle-immobilized substrate compared with HHH. In a separate set of simulations, we predict the structures of the adsorbed tripeptides at the two aqueous Au facets, revealing facet-dependent differences in the adsorbed conformations. Our findings suggest that Au facet effects, where relevant, may influence the adsorption structures and energetics of biomolecules, highlighting the possible influence of the structural model used to interpret experimental binding data. / Air Office of Scientific Research, Grant No. FA9550-12-1-0226

Thesis (MSc (Earth Sciences))--Stellenbosch University, 2008. / Detailed geological mapping and a structural analysis of auriferous quartz veins were undertaken in the Karibib region of the Pan-African Damara belt in central Namibia. The study focuses on the formation and controls of quartz-vein sets and associated lodegold mineralization in heterogeneous, siliciclastic- and marble- dominated amphibolitefacies host rocks around the Navachab gold mine and adjacent areas. Two main arrays of shallowly-dipping quartz veins can be distinguished that form a conjugate set. Steep, bedding-parallel and high-angle cross-cutting veins also occur, but play a subordinate role for mineralization. The orientation of the main conjugate set and progressive deformation of these quartz veins indicate that veining occurred during the late stages of the main phase of NW-SE directed, subhorizontal shortening (D2) and associated NW-verging folding and top-to-the-NW thrusting. Cross-cutting relationships with plutonic rocks indicate a timing of ca. 540 Ma for the mineralization. The quartz veins sets show a consistent orientation irrespective of their location with respect to NE-trending, NW-verging first-order fold structures that were previously considered to be pertinent for the mineralization. The quartz vein sets also cross-cut different lithologies at high angles. This suggests that the regional strain (D2) was the first-order control of quartz vein formation. More localized lithological and/or structural controls played, however, an important factor for the formation of economicgrade mineralization. Thick and closely spaced quartz veins in steeply dipping rocks of the Navachab open pit form a more than 150m thick economic-grade vein swarm. In this structural situation and during layer-normal subhorizontal shortening, the host rocks experienced high extensional strains in a vertical direction, favouring the formation of subhorizontal extension fractures.

M.Phil. (Mineral Economics) / This work is an attempt to discover whether or not South Africa's gold reserves have been properly exploited - has the wealth that has been removed been used to the best advantage. It became apparent to the author whilst conducting feasibility studies on both projected and operating mines that scant attention is paid to the determination of an optimal time path of depletion for a mineral deposit by the planners. The main, if not sole, criterion is the maximising of returns on the capital invested. The thesis proposes a methodology to describe the actual depletion paths achieved by a selection of South African gold mines. The work of mineral economists, especially Harold Hotelling, is used to provide a theoretical base for the. proposals. The mines were selected to cover as wide a range of the exploitation cycle as possible from the planning stage to final abandonment.

This Thesis reports the synthesis, purification and characterisation of gold nanoparticles (NPs) functionalised with a monolayer of hydrazone ligands in order to perform post-synthetic manipulations of the NP-bound monolayer exploiting dynamic covalent chemistry. NP post-synthetic manipulation based on reversible non-covalent interactions between oligonucleotides represents a promising approach to achieve functionalisation and self-assembly for potential applications in biology and medicine. However, the stability of these nanosystems is ensured only in a narrow window of environmental conditions. On the other hand, irreversible covalent strategies potentially allow the full range of synthetic chemistry to be exploited but they provide poor control over the manipulation of the NP-bound monolayer and can only produce kinetically controlled amorphous NP aggregates. Dynamic covalent chemistry represents an interesting and an attractive alternative approach because it would combine the reversibility of non-covalent interactions with the stability of covalent bonds. By this way, ligand-functionalised NPs could be manipulated in order to introduce a large variety of molecular functionalities on the NP surface not only to subtly tune the NP physicochemical properties but also to access an entire range of novel nanomaterials.

Ore deposits of the Krásná Hora ore district are the main representative of the Sb-Au mineralization in the Czech Republic. It can be classified genetically as epizonal subtype of orogenic gold deposits. Spatially and partly temporally are associated with the intrusion of the Central Bohemian Pluton. The ore bodies are related to quartz veins that follow the course of E-W striking lamprophyre dykes, which are usually heavily crushed and altered. Ore shoots with massive stibnite are located mainly at the intersections of these E-W trending veins with the NW-SE striking tectonic fault zones. Au-Sb ores at Krásná Hora ore district formed in an area of repeatedly activated fault zones. Three generations of hydrothermal quartz were identified on microscopic scale. Earliest quartz (Qtz1), which was considered in the literature auriferous originated from low-salinity H2O - CO2 fluids at ~350 řC and at a depth of about 5 km. The younger quartz (Qtz2) originated at lower temperatures of about 260 řC and lower depth of about 3-4 km from low/saline aqueous fluids. Both older (Qtz1) and younger quartz (Qtz2) are not auriferous. The gold is associated with younger paragenetic formation (Anti + Au + Cc + Qtz3) that fills in intergranular spaces and fractures in Qtz1 and Qtz2 . Due to the partial exhumation of the...

Cette thèse comporte trois parties principales : la première concerne la synthèse et la fonctionnalisation des nanoparticules (NPs) d’or de forme sphérique et cylindrique. Les NPs d’or sont obtenues par réduction d’un sel métallique. En faisant varier certains paramètres de synthèse tels que la concentration en sels et/ou la concentration en réducteur, on peut facilement ajuster la taille de NPs sphériques. Bien qu’il existe diverses méthodes permettant de préparer des NPs cylindriques, il subsiste un problème de reproductibilité basée sur la pureté des produits de synthèse. Les différentes analyses de CTAB nous ont permis de proposer des solutions à ce problème. La fonctionnalisation de la surface des NPs d’or permet d’apporter à ces dernières de nouvelles propriétés tout en conservant leurs propriétés intrinsèques. Le but de cette fonctionnalisation est de modifier la surface des NPs en fonction des applications visées. Nous présentons ainsi différentes études de fonctionnalisation par des polyélectrolytes (PEI et PSS), des couches oxydes de SiO2, et de TiO2 et par le TDBC. La réponse optique des NPs d’or étant sensible à l’indice de réfraction du milieu environnant, il est possible de suivre et de quantifier cette fonctionnalisation par spectroscopie d’absorption. Dans une seconde partie, nous avons développé une voie de synthèse simple permettant de préparer le cœur coquille Au@TDBC sans ajout supplémentaire de sels ou de bases et à température ambiante. Etant donné qu’il est possible de moduler la taille des particules, l’optimisation du couplage fort entre les transitions électroniques du TDBC et les modes plasmon de résonances des Nps d’Au a été obtenu correspondant à une énergie de Rabi de 220 meV valeur qui n’a pas encore été obtenue avec un tel système. Dans une troisième partie, nous avons développé une nouvelle approche basée sur la méthode de Stöber pour fonctionnaliser les NPs avec des couches d’oxyde de SiO2 et de TiO2. L’utilisation des systèmes Au@TiO2 est une perspective intéressante en photocatalyse car le contact entre le métal et le semi-conducteur devrait entrainer une nette augmentation de l’efficacité photocatalytique. En effet, le métal agit comme un réservoir de photoélectrons améliorant le transfert de charges interfaciales tout en retardant la recombinaison des paires électrons-trous photo excités du semi-conducteur. / This thesis has three main parts: the first part relates to the synthesis and the functionalization of spherical gold nanoparticles (NPs) and nanorods. Gold NPs are obtained by chemical reduction of gold salt. By varying some synthesis parameters such as gold salt concentration and or reducing agent concentration, we can easily adjust the size of gold NPs. Different methods can be used to prepare gold nanorods, but there is a problem of reproducibility. This problem is based on the purity of products used to prepare gold nanorods. Different analysis of CTAB allowed us to propose solutions to this problem. Functionalization brings to gold NPs new properties. The aim of the functionalization is to modify the surface of gold NPs based on the intended applications. We present various functionalization of Au NPs by polyelectrolytes (PEI and PSS), oxides (SiO2 and TiO2) and TDBC. The optical response of Au NPs is sensitive to the refractive indexe of the surrounding medium, it is then possible to monitor and quantify this functionalization by absorption spectroscopy. In the second part of this work, we have developed a simple synthetic route for preparing Au@TDBC core shell without additional salts or bases at room temperature. Since it is possible to vary the particle size, optimization of the strong coupling between the electronic transitions of TDBC and the resonance plasmon of Au Nps obtained correspond to Rabi energy of 220 meV value which has not yet been achieved with such a system. In the third part, we have developed a new approach based on the Stöber method to functionalize the NPs with an oxide layer of SiO2 and TiO2. The use of Au@TiO2 core shell system is an interesting perspective in photocatalysis because the contact between metal and semiconductor should cause a marked increase in the photocatalytic efficiency. Indeed, the metal acts as a reservoir of photoelectrons improving the interfacial charge transfer while retarding the recombination of electron-hole pair of the semiconductor.

Ph.D. / Chapter 1 presents a brief overview on the development of platinum, ruthenium and gold anti-cancer complexes. The clinical success of cisplatin has been a tremendous impetus for the design of metal-based antitumor drugs. Its mechanism of action is therefore briefly discussed, as well as the toxic side effects of its clinical use and the cellular resistance to the drug. It is its side effects and drug resistance that have stimulated the development of cisplatin analogues and other metal based anti-cancer agents. Compounds showing most promise are ruthenium complexes which are structurally different but have the same stability and show similar modes of binding to DNA. The last part of the introduction deals with the development of gold(I) and gold(III) complexes, the main topics of the research described in this thesis. Chapter 2 reports on the attempted preparation of dppf and dippf gold(III) complexes. However, the reaction of these diphosphines with H[AuCl4] and Na[AuCl4] all led to isolation of gold(I) complexes (dppf)Au2X2 (X = Cl (1), Br (3)) and (dippf)Au2X2 (X = Cl (2), Br (4)). In an attempt to oxidize the gold(I) complexes, (dppf)Au2Br2 (3) and (dippf)Au2Br2 (4) were reacted with excess bromine yielding two new complexes (C5H4Br3)(PR2)AuBr (R = Ph, 5; R = i-Pr, 6). This bromination reaction could be extended to the ligands and bromination of the free diphosphinoferrocene ligands produced the expected brominated cyclopentenes (C5H4Br3)(PR2) (R = Ph, 7; R = i-Pr, 8) in good yields. However, these could not be complexed to gold due to reduced basicity of 7 and 8. When the bromination was performed under wet aerobic conditions the oxidized pseudo-centrosymmetric product, [doppf][FeBr4] (9) {doppf = 1,1’-bis(oxodiphenylphosphino)ferrocene, was obtained as the major product. Solid-state structures of 1, 2, 4, 6, and 9 were established by means of single-crystal X-ray crystallography. Chapter 3 reports on the use of chiral Josiphos and Walphos diphosphine ligands to form palladium, platinum and gold complexes. The platinum complexes were prepared by reacting the ligands with [PtCl2(cod)] while the palladium complexes were prepared from [PdCl2(NCMe)2]. The complexes obtained had the general formula [MCl2(P-P)], where M = Pd, Pt, and P-P = Josiphos or Walphos ligand, and were obtained in good yields. The X-ray structures of a palladium(II) and a platinum(II) complex of the same Josiphos ligand were determined. The Josiphos complexes 12 and 14 show good solubility in common solvents. Furthermore, the complexes remained soluble and stable in a 40:60 water:DMSO mixture. The Walphos complexes 13 and 15 rapidly precipitated under the same conditions. In line with this limited solubility 13 and 15 showed minimal cytotoxic effects when compared to their Josiphos counterparts 12 and 14 whose cytotoxic effects (in terms of IC50 values ) were six to seven times less than cisplatin. Reaction of the Walphos ligand and H[AuCl4] in a 1:1 ratio gave a dinuclear gold(I) complex 18 while the same reaction with Josiphos gave a mixture of intractable materials. However a 1:1 reaction of the Josiphos with AuCl(tht) gave a mononuclear three-coordinate gold(I) complex 16. A P^N chiral ligand comprising of a diphenylphosphine and a pyrazole moiety was also prepared and was complexed with AuCl(tht) to give a phosphine bound gold(I) complex 19. The structure of this complex was determined by X-ray studies. From the studies it became evident that apart from increasing the basicity of compound the pyrazolyl moiety remains dangling and the complex shows bond parameters similar to those observed with monophosphine ferrocenyl complexes. Chapter 4 reports on the bidentate and monodentate gold(III) complexes based on the (pyrazolylmethyl)pyridine ligands together with their platinum(II) complexes. The denticity of the complexes depended on the position of the pyrazolyl moiety relative to the pyridine nitrogen. When ortho-substituted ligands were reacted in a 1:1 ratio with H[AuCl4] in a mixture of water and ethanol at room temperature, bidentate cationic complexes of the general formula [AuCl2(PyCH2R2pz)][X], where R = Me (20), X = AuCl4-; R = Ph (21), X = Cl-; t-Bu (22), X= Cl- and p-tol (23), X = AuCl4-, were obtained. When para-substituted ligands were used under same reaction conditions, neutral monodentate complexes [AuCl3(PyCH2R2pz)], where R = Me (24) and R = Ph (25), were obtained. Platinum(II) complexes were obtained using K2[PtCl4] in a mixture of water and ethanol under reflux, and affords neutral complexes of the type [PtCl2(PyCH2R2pz)], where R = Me (27), Ph (28), t-Bu (29) and p-tol (30). When acetone was used instead of ethanol monoacetonylplatinum(II) complex (29a) was formed and on prolonged heating formation of the diacetonyl complex (28b) was observed. Both the platinum and the gold complexes were evaluated for their anti-cancer potency. The gold(III) complexes were devoid of any activity while the platinum complex 30 showed activity 8 times lower than cisplatin. The structures of 23, 25, 28, 29 and 29a were determined from single-crystal X-ray diffraction studies. In Chapter 5, tridentate complexes based on bis(pyrazolylethyl)amine are reported. These were prepared with the aim of improving water-solubility and cytotoxicity of the resulting complexes. New synthetic methods for preparation of the ligands NH(CH2CH2pz)2 (R = Me (L7), H (L8), t-Bu (L9)) under mild reaction conditions were developed albeit the yields obtained were generally low. The reaction of these ligands with H[AuCl4] gave corresponding tridentate dicationic gold(III) complexes [NH(CH2CH2pz)2][X]2 (R = Me (31), H (32), X = AuCl4 , and R = t-Bu (33), X = Cl-). Despite the ligands stabilizing the gold(III) ion, they showed no solubility in water. In an attempt to make the ligand system water soluble, a thiocarbamate analogue with pyrazolyl groups replaced by hydroxyl groups was prepared. However the resulting gold(III) complex [Au{CS2N(CH2CH2OH)2}2][AuCl2] (34) was found to be only soluble in DMSO.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, for the Degree of Doctor of Philosophy Johannesburg, 1995 / A different class of mesothermal gold deposit at Sabie-Pilgrim’s Rest is described which is probably associated with the Bushveld igneous event in South Africa. Pressure and temperature estimates indicate that the ore-fluids of the Sabie-Pilgrim's Rest Goldfield, which occurs within the early Proterozoic Transvaal Supergroup, were similar to those of mesothermal gold deposits. [Abbreviated abstract. Open document ot view full version]