Facet selectivity in gold binding peptides: exploiting interfacial water structure

Peptide sequences that can discriminate between gold facets under aqueous conditions offer a promising route to control the growth and organisation of biomimetically-synthesised gold nanoparticles. Knowledge of the interplay between sequence, conformations and interfacial properties is essential for predictable manipulation of these biointerfaces, but the structural connections between a given peptide sequence and its binding affinity remain unclear, impeding practical advances in the field. These structural insights, at atomic-scale resolution, are not easily accessed with experimental approaches, but can be delivered via molecular simulation. A current unmet challenge lies in forging links between predicted adsorption free energies derived from enhanced sampling simulations with the conformational ensemble of the peptide and the water structure at the surface. To meet this challenge, here we use an in situ combination of Replica Exchange with Solute Tempering with Metadynamics simulations to predict the adsorption free energy of a gold-binding peptide sequence, AuBP1, at the aqueous Au(111), Au(100)(1 × 1) and Au(100)(5 × 1) interfaces. We find adsorption to the Au(111) surface is stronger than to Au(100), irrespective of the reconstruction status of the latter. Our predicted free energies agree with experiment, and correlate with trends in interfacial water structuring. For gold, surface hydration is predicted as a chief determining factor in peptide-surface recognition. Our findings can be used to suggest how shaped seed-nanocrystals of Au, in partnership with AuBP1, could be used to control AuNP nanoparticle morphology.

Stretching of BDT-gold molecular junctions: thiol or thiolate termination?

It is often assumed that the hydrogen atoms in the thiol groups of a benzene-1,4-dithiol dissociate when Au-benzene-1,4-dithiol-Au junctions are formed. We demonstrate, by stability and transport property calculations, that this assumption cannot be made. We show that the dissociative adsorption of methanethiol and benzene-1,4-dithiol molecules on a flat Au(111) surface is energetically unfavorable and that the activation barrier for this reaction is as high as 1 eV. For the molecule in the junction, our results show, for all electrode geometries studied, that the thiol junctions are energetically more stable than their thiolate counterparts. Due to the fact that density functional theory (DFT) within the local density approximation (LDA) underestimates the energy difference between the lowest unoccupied molecular orbital and the highest occupied molecular orbital by several electron-volts, and that it does not capture the renormalization of the energy levels due to the image charge effect, the conductance of the Au-benzene-1,4-dithiol-Au junctions is overestimated. After taking into account corrections due to image charge effects by means of constrained-DFT calculations and electrostatic classical models, we apply a scissor operator to correct the DFT energy level positions, and calculate the transport properties of the thiol and thiolate molecular junctions as a function of the electrode separation. For the thiol junctions, we show that the conductance decreases as the electrode separation increases, whereas the opposite trend is found for the thiolate junctions. Both behaviors have been observed in experiments, therefore pointing to the possible coexistence of both thiol and thiolate junctions. Moreover, the corrected conductance values, for both thiol and thiolate, are up to two orders of magnitude smaller than those calculated with DFT-LDA. This brings the theoretical results in quantitatively good agreement with experimental data.

Ethanol and Water Adsorption on Close-Packed 3d, 4d, and 5d Transition-Metal Surfaces: A Density Functional Theory Investigation with van der Waals Correction

Nowadays, there is a great interest in the economic success of direct ethanol fuel cells; however, our atomistic understanding of the designing of stable and low-cost catalysts for the steam reforming of ethanol is still far from satisfactory, in particular due to the large number of undesirable intermediates. In this study, we will report a first-principles investigation of the adsorption properties of ethanol and water at low coverage on close-packed transition-metal (TM) surfaces, namely, Fe(110), Co(0001), Ni(111), Cu(111), Ru(0001), Rh(111), Pd(111), Ag(111), Os(0001), Ir(111), Pt(111), and Au(111), employing density functional theory (DFT) calculations. We employed the generalized gradient approximation with the formulation proposed by Perdew, Burke, and Erzenholf (PBE) to the exchange correlation functional and the empirical correction proposed by S. Grimme (DFT+D3) for the van der Waals correction. We found that both adsorbates binds preferentially near or on the on top sites of the TM surfaces through the 0 atoms. The PBE adsorption energies of ethanol and water decreases almost linearly with the increased occupation of the 4d and 5d d-band, while there is a deviation for the 3d systems. The van der Waals correction affects the linear behavior and increases the adsorption energy for both adsorbates, which is expected as the van der Waals energy due to the correlation effects is strongly underestimated by DFT-PBE for weak interacting systems. The geometric parameters for water/TM are not affected by the van der Waals correction, i.e., both DFT and DFT+D3 yield an almost parallel orientation for water on the TM surfaces; however, DFT+D3 changes drastically the ethanol orientation. For example, DFT yields an almost perpendicular orientation of the C-C bond to the TM surface, while the C-C bond is almost parallel to the surface using DFT +D3 for all systems, except for ethanol/Fe(110). Thus, the van der Waals correction decreases the distance of the C atoms to the TM surfaces, which might contribute to break the C-C bond. The work function decreases upon the adsorption of ethanol and water, and both follow the same trends, however, with different magnitude (larger for ethanol/TM) due to the weak binding of water to the surface. The electron density increases mainly in the region between the topmost layer and the adsorbates, which explains the reduction of the substrate work function.

Rastertunnelmikroskopie kombiniert mit optischen Methoden und ihre Anwendung für opto-elektronische Experimente an nanoskopischen Strukturen

Die vorliegende Arbeit untersucht mittels lichtunterstützter Tunnelmikroskopie (STM) den Elektronentransport in farbstoffbedeckten, nanoporösen TiO2-Schichten, die in photoelektrochemischen Solarzellen eingesetzt werden. Transportrelevante Eigenschaften wie die elektronische Zustandsdichte sowie lichtinduzierte Vorgänge wie der Aufbau einer lichtinduzierten Oberflächenladung und lokale Photoströme werden ortsaufgelöst gemessen. Für einen möglichen Einsatz in lichtunterstützter Tunnelmikroskopie werden desweiteren Gold-Nanopartikel auf einer Amino-Hexanthiol-Monolage auf Coulomb-Blockaden untersucht. Den zweite Schwerpunkt stellen methodische Arbeiten zur Messung optischer Nahfelder in STM-Experimenten dar. Erstens sollen die Vorteile von Apertur- und aperturloser optischer Rasternahfeld-Mikroskopie mit komplett metallisierten Faserspitzen verbunden werden, die durch die Faser beleuchtet werden. Es gelingt nicht, theoretisch vorhergesagte hohe optische Auflösungen zu bestätigen. Zweitens werden transparente Spitzen aus Sb-dotiertem Zinnoxid erfolgreich als Tunnelspitzen getestet. Die Spitzen ermöglichen STM-Elektrolumineszenz-Experimente zur Charakterisierung optischer Nahfelder, ohne diese durch eine metallische Spitze zu beeinträchtigen. In einer STM-Studie wird das Selbstorganisations-Verhalten von Oktanthiol und Oktandithiol auf Au(111) aus Ethanol untersucht. Bei geringer relativer Konzentration der Dithiole (1:2000), bildet sich eine Phase liegender Dithiole, deren Ordnung durch die Präsenz der Oktanthiole katalysiert wird. Schließlich wird ein als 'dynamische Tunnelmikroskopie' bezeichneter Modus für die Tunnelmikroskopie in elektrisch leitfähiger Umgebung erfolgreich getestet, der zur Unterdrückung des elektrochemischen Leckstromanteils die Ableitung des Stroms nach dem Abstand als STM-Abstandssignal verwendet.

Two-dimensional assembly and local redox-activity of molecular hybrid structures in an electrochemical environment

The self-assembly and redox-properties of two viologen derivatives, N-hexyl-N-(6-thiohexyl)-4,4-bipyridinium bromide (HS-6V6-H) and N,N-bis(6-thiohexyl)-4,4-bipyridinium bromide (HS-6V6-SH), immobilized on Au(111)-(1x1) macro-electrodes were investigated by cyclic voltammetry, surface enhanced infrared spectroscopy (SEIRAS) and in situ scanning tunneling microscopy (STM). Depending on the assembly conditions one could distinguish three different types of adlayers for both viologens: a low coverage disordered and an ordered striped phase of flat oriented molecules as well as a high coverage monolayer composed of tilted viologen moieties. Both molecules, HS-6V6-H and HS-6V6-SH, were successfully immobilized on Au(poly) nano-electrodes, which gave a well-defined redox-response in the lower pA–current range. An in situ STM configuration was employed to explore electron transport properties of single molecule junctions Au(T)|HS-6V6-SH(HS-6V6-H)|Au(S). The observed sigmoidal potential dependence, measured at variable substrate potential ES and at constant bias voltage (ET–ES), was attributed to electronic structure changes of the viologen moiety during the one-electron reduction/re-oxidation process V2+ V+. Tunneling experiments in asymmetric, STM-based junctions Au(T)-S-6V6-H|Au(S) revealed current (iT)–voltage (ET) curves with a maximum located at the equilibrium potential of the redox-process V2+ V+. The experimental iT–ET characteristics of the HS-6V6-H–modified tunneling junction were tentatively attributed to a sequential two-step electron transfer mechanism.

Electronic band dispersion of graphene nanoribbons via Fourier-transformed scanning tunneling spectroscopy

The electronic structure of atomically precise armchair graphene nanoribbons of width N=7 (7-AGNRs) are investigated by scanning tunneling spectroscopy (STS) on Au(111). We record the standing waves in the local density of states of finite ribbons as a function of sample bias and extract the dispersion relation of frontier electronic states by Fourier transformation. The wave-vector-dependent contributions from these states agree with density functional theory calculations, thus enabling the unambiguous assignment of the states to the valence band, the conduction band, and the next empty band with effective masses of 0.41±0.08me,0.40±0.18me, and 0.20±0.03me, respectively. By comparing the extracted dispersion relation for the conduction band to corresponding height-dependent tunneling spectra, we find that the conduction band edge can be resolved only at small tip-sample separations and has not been observed before. As a result, we report a band gap of 2.37±0.06 eV for 7-AGNRs adsorbed on Au(111).

Crystallographic orientation and electrode nature are key factors for electric current generation by Geobacter sulfurreducens

We have investigated the influence of electrode material and crystallographic structure on electron transfer and biofilm formation of Geobacter sulfurreducens. Single-crystal gold - Au(110), Au(111), Au(210) - and platinum - Pt(100), Pt(110), Pt(111), Pt(210) - electrodes were tested and compared to graphite rods. G. sulfurreducens electrochemically interacts with all these materials with different attachment kinetics and final current production, although redox species involved in the electron transfer to the anode are virtually the same in all cases. Initial bacterial colonization was fastest on graphite up to the monolayer level, whereas gold electrodes led to higher final current densities. Crystal geometry showed to have an important influence, with Au(210) sustaining a current density of up to 1442 (± 101) μA cm- 2 at the steady state, over Au(111) with 961 (± 94) μA cm- 2 and Au(110) with 944 (± 89) μA cm- 2. On the other hand, the platinum electrodes displayed the lowest performances, including Pt(210). Our results indicate that both crystal geometry and electrode material are key parameters for the efficient interaction of bacteria with the substrate and should be considered for the design of novel materials and microbial devices to optimize energy production.

Development of calix[4]arene-functionalized microcantilever array sensing system for the rapid, sensitive and simultaneous detection of metal ions in aqueous solutions

The work described in this thesis was conducted with the aim of: 1) investigating the binding capabilities of calix[4]arene-functionalized microcantilevers towards specific metal ions and 2) developing a new16-microcantilever array sensing system for the rapid, and simultaneous detection of metal ions in fresh water. Part I of this thesis reports on the use of three new bimodal calix[4]arenes (methoxy, ethoxy and crown) as potential host/guest sensing layers for detecting selected ions in dilute aqueous solutions using single microcantilever experimental system. In this work it was shown that modifying the upper rim of the calix[4]arenes with a thioacetate end group allow calix[4]arenes to self-assemble on Au(111) forming complete highly ordered monolayers. It was also found that incubating the microcantilevers coated with 5 nm of Inconel and 40 nm of Au for 1 h in a 1.0 M solution of calix[4]arene produced the highest sensitivity. Methoxy-functionalized microcantilevers showed a definite preference for Ca²⁺ ions over other cationic guests and were able to detect trace concentration as low as 10⁻¹² M in aqueous solutions. Microcantilevers modified with ethoxy calix[4]arene displayed their highest sensitivity towards Sr²⁺ and to a lesser extent Ca²⁺ ions. Crown calix[4]arene-modified microcantilevers were however found to bind selectively towards Cs⁺ ions. In addition, the counter anion was also found to contribute to the deflection. For example methoxy calix[4]arene-modified microcantilever was found to be more sensitive to CaCl₂ over other water-soluble calcium salts such as Ca(NO₃)₂ , CaBr₂ and CaI₂. These findings suggest that the response of calix[4]arene-modified microcantilevers should be attributed to the target ionic species as a whole instead of only considering the specific cation and/or anion. Part II presents the development of a 16-microcantilever sensor setup. The implementation of this system involved the creation of data analysis software that incorporates data from the motorized actuator and a two-axis photosensitive detector to obtain the deflection signal originating from each individual microcantilever in the array. The system was shown to be capable of simultaneous measurements of multiple microcantilevers with different coatings. A functionalization unit was also developed that allows four microcantilevers in the array to be coated with an individual sensing layer one at the time. Because of the variability of the spring constants of different cantilevers within the array, results presented were quoted in units of surface stress unit in order to compare values between the microcantilevers in the array.

The nature of alkanethiol self-assembled monolayer adsorption on sputtered gold substrates

A detailed study of the self-assembly and coverage by 1-nonanethiol of sputtered Au surfaces using molecular resolution atomic force microscopy (AFM) and scanning tunneling microscopy (STM) is presented. The monolayer self-assembles on a smooth Au surface composed predominantly of {111} oriented grains. The domains of the alkanethiol monolayer are observed with sizes typically of 5-25 nm, and multiple molecular domains can exist within one Au grain. STM imaging shows that the (4 × 2) superlattice structure is observed as a (3 × 2√3) structure when imaged under noncontact AFM conditions. The 1-nonanethiol molecules reside in the threefold hollow sites of the Au{111} lattice and aligned along its lattice vectors. The self-assembled monolayer (SAM) contains many nonuniformities such as pinholes, domain boundaries, and monatomic depressions which are present in the Au surface prior to SAM adsorption. The detailed observations demonstrate limitations to the application of 1-nonanethiol as a resist in atomic nanolithography experiments to feature sizes of ∼20 nm.

Design and Implementation of Tools for STM Studies in UHV and at the Solid-Liquid Interface

This thesis presents details of the design and development of novel tools and instruments for scanning tunneling microscopy (STM), and may be considered as a repository for several years' worth of development work. The author presents design goals and implementations for two microscopes. First, a novel Pan-type STM was built that could be operated in an ambient environment as a liquid-phase STM. Unique features of this microscope include a unibody frame, for increased microscope rigidity, a novel slider component with large Z-range, a unique wiring scheme and damping mechanism, and a removable liquid cell. The microscope exhibits a high level of mechanical isolation at the tunnel junction, and operates excellently as an ambient tool. Experiments in liquid are on-going. Simultaneously, the author worked on designs for a novel low temperature, ultra-high vacuum (LT-UHV) instrument, and these are presented as well. A novel stick-slip vertical coarse approach motor was designed and built. To gauge the performance of the motor, an in situ motion sensing apparatus was implemented, which could measure the step size of the motor to high precision. A new driving circuit for stick-slip inertial motors is also presented, that o ffers improved performance over our previous driving circuit, at a fraction of the cost. The circuit was shown to increase step size performance by 25%. Finally, a horizontal sample stage was implemented in this microscope. The build of this UHV instrument is currently being fi nalized. In conjunction with the above design projects, the author was involved in a collaborative project characterizing N-heterocyclic carbene (NHC) self-assembled monolayers (SAMs) on Au(111) films. STM was used to characterize Au substrate quality, for both commercial substrates and those manufactured via a unique atomic layer deposition (ALD) process by collaborators. Ambient and UHV STM was then also used to characterize the NHC/Au(111) films themselves, and several key properties of these films are discussed. During this study, the author discovered an unexpected surface contaminant, and details of this are also presented. Finally, two models are presented for the nature of the NHC-Au(111) surface interaction based on the observed film properties, and some preliminary theoretical work by collaborators is presented.

Mercury vapor sorption and amalgamation with a thin gold film

Understanding the amalgamation mechanisms between mercury and gold is of fundamental interest and importance to many mercury sensing applications. However, there is only limited and piecemeal discussion in the literature of the mechanisms by which Au-Hg amalgams are formed on thin Au films. Here, we present a comprehensive description of a series of morphological changes occurring in a thin polycrystalline Au film during Au-Hg amalgamation investigated by scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and atomic force microscopy (AFM). These microscopic investigations enable us to offer a coherent explanation for the features and the mechanisms of amalgamation of Hg with Au in the film. We also use an optical technique (fringes of equal chromatic order, FECO) to observe changes in optical thickness and reflectivity of the film. Amalgamation reactions in the film render it inhomogeneous, thus making optical techniques unsuitable as a method for quantitative monitoring of Hg vapor using Au films of this type.

Theoretical study of interaction between atoms of Au, Ag, Cu and clean Si(111) surface

To evaluate the interactions between the atoms of An, Ag and Cu and clean Si(111) surface, two types of silicon clusters Si4H7 and Si16H20 together with their metal complexes were studied by using hybrid (U)B3LYP density functional theory method. Optimized geometries and energies on different adsorption sites indicate that: (1) the binding energies at different adsorption sites are large (ranging from similar to 1.2 to 2.6 eV depend on the metal atoms and adsorption sites), suggesting a strong interaction between metal atom and silicon surface; (2) the most favorable adsorption site is the on top (T) site. Mulliken population analysis indicated that in the system of on top (T) site, a covalent bond is formed between metal atom and dangling bond of surface Si atom. (c) 2006 Elsevier B.V. All rights reserved.

Au on (111) and (110) surfaces of CeO2: A density-functional theory study

The atomic structures of gold supported on (111) and (110) surfaces of CeO2 have been studied using density-functional theory calculations. A single Au atom is placed on three adsorption sites on the surfaces; the stoichiometric surfaces, an oxygen vacancy and a Ce-vacancy. It is found that (i) the Au adsorption energies are in the following order: E-ad(Ce-vacancy) > E-ad(O-vacancy) > E-ad(stoichiometric surface); and (ii) the Au atom adsorption on the Ce-vacancy activates O atoms nearby. One 0 atom is less stable than that in O-2 in the gas phase and another O atom is much easier to remove compared to that of the stoichiometric surfaces. These results suggest that the Au adsorption on Ce-vacancies not only creates an O-vacancy but also activates an O atom nearby. This provides a piece of direct evidence that Au adsorption on a Ce-vacancy may be responsible for some unique catalytic properties of Au/CeO2. (C) 2008 Elsevier B.V. All rights reserved.

New insight into mechanisms in water-gas-shift reaction on Au/CeO2(111): A density functional theory and kinetic study

Using density functional theory (DFT) and kinetic analyses, a new carboxyl mechanism for the water-gas-shift reaction (WGSR) on Au/CeO2(111) is proposed. Many elementary steps in the WGSR are studied using an Au cluster supported on CeO2(111). It is found that (i) water can readily dissociate at the interface between Au and CeO2; (ii) CO2 can be produced via two steps: adsorbed CO on the Au cluster reacts with active OH on ceria to form the carboxyl (COOH) species and then COOH reacts with OH to release CO2; and (iii) two adsorbed H atoms recombine to form molecular H-2 on the Au cluster. Our kinetic analyses show that the turnover frequency of the carboxyl mechanism is consistent with the experimental one while the rates of redox and formate mechanisms are much slower than that of carboxyl mechanism. It is suggested that the carboxyl pathway is likely to be responsible for WGSR on Au/CeO2.

Ensemble effects in the coupling of acetylene to benzene on a bimetallic surface: A study with Pd{111}/Au

Acetylene coupling to benzene on the Pd(lll) surface is greatly enhanced by the presence of catalytically inert Au atoms. LEED and Auger spectroscopy show that progressive annealing of Au overlayers on Pd(lll) leads to the formation of a series of random surface alloys with continuously varying composition. Cyclization activity is a strong function of surface composition-the most efficient catalyst corresponds to a surface of composition similar to 85% Pd. CO TPD and HREELS data show that acetylene cyclization activity is not correlated with the availability of singleton Pd atoms, nor just with the presence of 3-fold pure Pd sites-the preferred chemisorption site for C2H2 on Pd{111}. The data can be quantitatively rationalized in terms of a simple model in which catalytic activity is dominated by Pd6Au and Pd-7 surface ensembles, allowance being made for the known degree to which pure Pd{111} decomposes the reactant and product molecules.