A periodic charge-dipole electrostatic model: parametrization for silver slabs

We present an extension of the charge-dipole model for the description of periodic systems. This periodic charge-dipole electrostatic model (PCDEM) allows one to describe the linear response of periodic structures in terms of charge- and dipole-type gaussian basis functions. The long-range electrostatic interaction is efficiently described by means of the continuous fast multipole method. As a first application, the PCDEM method is applied to describe the polarizability of silver slabs. We find that for a correct description of the polarizability of the slabs both charges and dipoles are required. However a continuum set of parametrizations, i.e., different values of the width of charge- and dipole-type gaussians, leads to an equivalent and accurate description of the slabs polarizability but a completely unphysical description of induced charge-density inside the slab. We introduced the integral squared density measure which allows one to obtain a unique parametrization which accurately describes both the polarizability and the induced density profile inside the slab. Finally the limits of the electrostatic approximations are also pointed out.

Electrochemical, high-resolution photoemission spectroscopy and vdW-DFT study of the thermal stability of benzenethiol and benzeneselenol monolayers on Au(111)

The preparation and thermal stability of benzenethiol and benzeneselenol self-assembled monolayers (SAMs) grown on Au(111) have been investigated by electrochemical experiments and high-resolution photoemission spectroscopy. Both techniques confirm the formation of monolayers with high packing densities (θ = 0.27-0.29 ML) and good degrees of order in both cases. Despite many similarities between the two SAMs, the thermal desorption is distinctly different: whereas the benzenethiol SAM desorbs in a single steplike process, the desorption of the benzeneselenol SAM occurs with a much lower activation energy and involves the cleavage of some Se-C bonds and a change in molecular configuration from standing up to lying down. This behavior is explained by considering the different nature of the bonding of the headgroup with the metal surface and with the phenyl ring. Density functional theory calculations show that the breakage of the Se-C bond has a lower activation energy barrier than the breakage of the S-C bond.

The chemistry of the sulfur-gold interface: in search of a unified model

Over the last three decades, self-assembled molecular films on solid surfaces have attracted widespread interest as an intellectual and technological challenge to chemists, physicists, materials scientists, and biologists. A variety of technological applications of nanotechnology rely on the possibility of controlling topological, chemical, and functional features at the molecular level. Self-assembled monolayers (SAMs) composed of chemisorbed species represent fundamental building blocks for creating complex structures by a bottom-up approach. These materials take advantage of the flexibility of organic and supramolecular chemistry to generate synthetic surfaces with well-defined chemical and physical properties. These films already serve as structural or functional parts of sensors, biosensors, drug-delivery systems, molecular electronic devices, protecting capping for nanostructures, and coatings for corrosion protection and tribological applications. Thiol SAMs on gold are the most popular molecular films because the resulting oxide-free, clean, flat surfaces can be easily modified both in the gas phase and in liquid media under ambient conditions. In particular, researchers have extensively studied SAMs on Au(111) because they serve as model systems to understand the basic aspects of the self-assembly of organic molecules on well-defined metal surfaces. Also, great interest has arisen in the surface structure of thiol-capped gold nanoparticles (AuNPs) because of simple synthesis methods that produce highly monodisperse particles with controllable size and a high surface/volume ratio. These features make AuNPs very attractive for technological applications in fields ranging from medicine to heterogeneous catalysis. In many applications, the structure and chemistry of the sulfur-gold interface become crucial since they control the system properties. Therefore, many researchers have focused on understanding of the nature of this interface on both planar and nanoparticle thiol-covered surfaces. However, despite the considerable theoretical and experimental efforts made using various sophisticated techniques, the structure and chemical composition of the sulfur-gold interface at the atomic level remains elusive. In particular, the search for a unified model of the chemistry of the S-Au interface illustrates the difficulty of determining the surface chemistry at the nanoscale. This Account provides a state-of-the-art analysis of this problem and raises some questions that deserve further investigation.

The golden pathway to thiolate-stabilized nanoparticles: following the formation of gold(I) thiolate from gold(III) chloride

Pathways for the formation of gold thiolate complexes from gold(III) chloride precursors AuCl(4)(-) and AuCl(3) are examined. This work demonstrates that two distinct reaction pathways are possible; which pathway is accessible in a given reaction may depend on factors such as the residue group R on the incoming thiol. Density functional theory calculations using the BP86 functional and a polarized triple-ζ basis set show that the pathway resulting in gold(III) reduction is favored for R = methyl. A two-to-one ratio of thiol or thiolate to gold can reduce Au(III) to Au(I), and a three-to-one ratio can lead to polymeric Au(SR) species, which was first suggested by Schaaff et al. J. Phys. Chem. B, 1997, 101, 7885 and later confirmed by Goulet and Lennox J. Am. Chem. Soc., 2010, 132, 9582. Most transition states in the pathways examined here have reasonable barrier heights around 0.3 eV; we find two barrier heights that differ substantially from this which suggest the potential for kinetic control in the first step of thiolate-protected gold nanoparticle growth.

Large-scale atomistic simulations of environmental effects on the formation and properties of molecular junctions

Using an updated simulation tool, we examine molecular junctions composed of benzene-1,4-dithiolate bonded between gold nanotips, focusing on the importance of environmental factors and interelectrode distance on the formation and structure of bridged molecules. We investigate the complex relationship between monolayer density and tip separation, finding that the formation of multimolecule junctions is favored at low monolayer density, while single-molecule junctions are favored at high density. We demonstrate that tip geometry and monolayer interactions, two factors that are often neglected in simulation, affect the bonding geometry and tilt angle of bridged molecules. We further show that the structures of bridged molecules at 298 and 77 K are similar.

Immobilization of monolayer protected lipophilic gold nanorods on a glass surface

We present a novel process of immobilization of gold nanorods (GNRs) on a glass surface. We demonstrate that by exploiting monolayer protection of the GNRs, their unusual optical properties can be completely preserved. UV-visible spectroscopy and atomic force microscopy analysis are used to reveal the optical and morphological properties of monolayer protected immobilized lipophilic GNRs, and molecular dynamics simulations are used to elucidate their surface molecule arrangements.

Nucleation and island growth of alkanethiolate ligand domains on gold nanoparticles

The metal oxide cluster α-AlW(11)O(39)(9-) (1), readily imaged by cryogenic transmission electron microscopy (cryo-TEM), is used as a diagnostic protecting anion to investigate the self-assembly of alkanethiolate monolayers on electrostatically stabilized gold nanoparticles in water. Monolayers of 1 on 13.8 ± 0.9 nm diameter gold nanoparticles are displaced from the gold surface by mercaptoundecacarboxylate, HS(CH(2))(10)CO(2)(-) (11-MU). During this process, no aggregation is observed by UV-vis spectroscopy, and the intermediate ligand-shell organizations of 1 in cryo-TEM images indicate the presence of growing hydrophobic domains, or "islands", of alkanethiolates. UV-vis spectroscopic "titrations", based on changes in the surface plasmon resonance upon exchange of 1 by thiol, reveal that the 330 ± 30 molecules of 1 initially present on each gold nanoparticle are eventually replaced by 2800 ± 30 molecules of 11-MU. UV-vis kinetic data for 11-MU-monolayer formation reveal a slow phase, followed by rapid self-assembly. The Johnson, Mehl, Avrami, and Kolmogorov model gives an Avrami parameter of 2.9, indicating continuous nucleation and two-dimensional island growth. During nucleation, incoming 11-MU ligands irreversibly displace 1 from the Au-NP surface via an associative mechanism, with k(nucleation) = (6.1 ± 0.4) × 10(2) M(-1) s(-1), and 19 ± 8 nuclei, each comprised of ca. 8 alkanethiolates, appear on the gold-nanoparticle surface before rapid growth becomes kinetically dominant. Island growth is also first-order in [11-MU], and its larger rate constant, k(growth), (2.3 ± 0.2) × 10(4) M(-1) s(-1), is consistent with destabilization of molecules of 1 at the boundaries between the hydrophobic (alkanethiolate) and the electrostatically stabilized (inorganic) domains.

Mass spectrometry and dynamics of gold adatoms observed on the surface of size-selected Au nanoclusters

We report the imaging, mass spectrum, and dynamical behavior of adatoms and small clusters observed on the surface facets of size-selected, truncated octahedral gold clusters, Au(N) (N = 923 ± 23), via aberration-corrected scanning transmission electron microscopy. Our quantitative atom counting measurements show that most (~70%) of the species on the surface are single Au adatoms. Such species are now proposed as key elements of the atomic structure of both monolayer-protected nanoclusters (nanoparticles) and self-assembled monolayers and may also play a role in gold nanocatalysis. The adatoms are found on both {100} and {111} facets with similar probabilities.

Physical structure of standing-up aromatic SAMs revealed by scanning tunneling microscopy

Long-range-ordered aromatic SAMs are formed on Au(111) using 4-nitrophenyl sulfenyl chloride as a precursor. Although the main structure is a √3 × √3 with a molecular density similar to that usually found for aliphatic SAMs, particular spots presenting specific shapes are also observed by STM. These include hexagons, partial hexagons, parallelograms, and zigzags resulting from specific arrangements of adsorbed molecules. These molecular arrangements are reversible as they form and dissociate or "vanish" in various areas on the surface. STM shows that these particular structures provide some order to their surrounding because areas void of these structures look less ordered. More interestingly, STM shows submolecular details of the molecules involved in forming these structures, hence providing direct experimental evidence for the ability of the STM to provide physical structure information of standing up SAMs. This is indeed a heavily debated question, and this work reports the first experimental example where submolecular physical structure is revealed by STM for standing-up SAMs.

Towards quantitative accuracy in first-principles transport calculations: The GW method applied to alkane/gold junctions

The calculation of the electronic conductance of nanoscale junctions from first principles is a long-standing problem in the field of charge transport. Here we demonstrate excellent agreement with experiments for the transport properties of the gold/alkanediamine benchmark system when electron-electron interactions are described by the many-body GW approximation. The conductance follows an exponential length dependence: G(n) = G(c) exp(-βn). The main difference from standard density functional theory (DFT) calculations is a significant reduction of the contact conductance, G(c), due to an improved alignment of the molecular energy levels with the metal Fermi energy. The molecular orbitals involved in the tunneling process comprise states delocalized over the carbon backbone and states localized on the amine end groups. We find that dynamic screening effects renormalize the two types of states in qualitatively different ways when the molecule is inserted in the junction. Consequently, the GW transport results cannot be mimicked by DFT calculations employing a simple scissors operator.

Dynamic double lattice of 1-adamantaneselenolate self-assembled monolayers on Au{111}

We report a complex, dynamic double lattice for 1-adamantaneselenolate monolayers on Au{111}. Two lattices coexist, revealing two different binding modes for selenols on gold: molecules at bridge sites have lower conductance than molecules at three-fold hollow sites. The monolayer is dynamic, with molecules switching reversibly between the two site-dependent conductance states. Monolayer dynamics enable adsorbed molecules to reorganize according to the underlying gold electronic structure over long distances, which facilitates emergence of the self-organized rows of dimers. The low-conductance molecules assume a (7 × 7) all-bridge configuration, similar to the analogous 1-adamantanethiolate monolayers on Au{111}. The high-conductance molecules self-organize upon mild annealing into distinctive rows of dimers with long-range order, described by a (6√5 × 6√5)R15° unit cell.

Reverse self-assembly: (111)-oriented gold crystallization at alkylthiol monolayer templates

It has long been known that thiol-terminated molecules self-assemble as commensurate monolayers on Au(111) surfaces. By spreading floating octadecanethiol monolayers on aqueous solutions of chloroauric acid (HAuCl4) and using x rays to reduce the gold ions as well as to probe the structure, we have observed the nucleation of (111)-oriented Au nanoparticles at thiol surfaces. This process may be similar to the formation of biogenic gold by bacteria. The thiol monolayer acts as a "soft template," changing its structure as Au crystals form so that there is a sqrt[3]×sqrt[3] commensurate relationship.

Ancillary nitrile substituents as convenient IR spectroscopic reporters for self-assembly of mercapto- and isocyanoazulenes on Au(111)

Synthesis and self-assembly of structurally related mercapto- and isocyanoazulenes, including novel 2-mercapto-1,3-dicyanoazulene (4) and 2-isocyano-1,3-dicyanoazulene (5), are reported. Exposing 5 adsorbed on Au(111) to a solution of 4 displaces the isocyanoazulene monolayer with that of the mercaptoazulene as judged by ν(C≡N) signatures of these films.

Phthalocyaninato complexes with peripheral alkylthio chains: disk-like adsorbate species for the vertical anchoring of ligands on gold surfaces

Thin metalorganic films were prepared on gold by self-assembly of thioether-functionalised phthalocyaninato complexes from solution. The phthalocyaninato ligands used contain eight peripheral, β-positioned, alkylthio substituents SR (1a: R = n-C(8)H(17), 1b: R = n-C(12)H(25)), which serve as headgroups for surface binding and promote lateral assembly, while the disk-like phthalocyaninato core offers the scope for the attachment of axial ligands to the adsorbed molecules. This process was mimicked by coordination of pyridine (Py) to [Zn(1a)] and [Zn(1b)], respectively. The crystal structures of the products [Zn(1a)(Py)] and [Zn(1b)(Py)] were determined. The crystal structures of 4,5-bis(octylthio)phthalodinitrile and 4,5-bis(dodecylthio)phthalodinitrile were also determined. The films fabricated from [Mn(1a)Cl] and [Mn(1b)Cl] on gold were characterised by XPS, ToF-SIMS and NEXAFS spectroscopy, which revealed the presence of well-defined and homogeneous self-assembled monolayers (SAMs), whose constituents are bound to the substrate by thioether-gold linkages. The orientation of the macrocycles is predominantly parallel to the surface. Strong electronic interaction of the manganese(III) centre with the substrate leads to Cl loss upon adsorption and its reduction to Mn(II).

Multidentate adsorbates for self-assembled monolayer films

The spontaneous adsorption of organic molecules on a variety of planar and nonplanar substrates, that is, self assembly, can generate films just one molecule thick. These nanoscale, self-assembled monolayer (SAM) films have been extensively used to engineer surfaces with well-defined properties. Their utility has been demonstrated in a wide range of applications, including wetting, adhesion, lubrication, patterning, and molecular recognition. Many SAM systems have been investigated, but alkanethiols adsorbed on gold are the most successful combination. This pairing offers a variety of advantages, including the ability to tune precisely the interfacial properties of a surface through the well-established organic synthetic methodologies that have been developed for preparing custom ω-terminated alkanethiols. Alkanethiolate monolayers are moderately stable at room temperature; however, these films degrade over time and readily desorb upon moderate heating. This shortcoming limits the use of SAMs in applications involving elevated temperatures or harsh environments. Accordingly, new adsorbates with multiple bonding moieties have been created to enhance the stability and versatility of SAMs. In this Account, we examine a variety of multidentate adsorbate structures that have been used to generate SAMs on planar substrates and on nanoparticles. Each of these chelating adsorbates (bidentates and tridentates) has been designed to generate well-defined organic monolayer films with multiple attachment points to the underlying substrate. This bonding arrangement allows the formation of SAMs with enhanced stability through the entropy-driven "chelate effect". The research examined here demonstrates that multidentate adsorbates provide robust films: they enable the use of SAMs under conditions that are incompatible with SAMs derived from normal alkanethiols. Another advantage offered by multidentate adsorbates is the capacity for new paradigms in thin-film composition. In particular, appropriately designed chelating adsorbates can be engineered to have two or more chemically distinct terminal groups that are covalently linked to the same underlying headgroup, without adding steric bulk that might prove detrimental to the resultant assembly. This strategy allows the generation of homogeneously mixed multicomponent surfaces, overcoming the problem of phase separation or "islanding" that is pervasive when two or more chemically distinct adsorbates are used to form mixed SAMs. Such homogeneously mixed films offer the opportunity to fine-tune the interfacial properties of a substrate and to create unique heterogeneous interfaces that are well defined by the chemical composition of the tailgroups exposed at the surface. The insight derived from these studies opens the door to new uses for SAMs, both in surface engineering applications (such as corrosion resistance and soft lithographic patterning) and in the stabilization and manipulation of nanoparticles.

Unifying interfacial self-assembly and surface freezing

X-ray investigations reveal that the monolayers formed at the bulk alkanol-sapphire interface are densely packed with the surface-normal molecules hydrogen bound to the sapphire. About 30-35 °C above the bulk, these monolayers both melt reversibly and partially desorb. This system exhibits balanced intermolecular and molecule-substrate interactions which are intermediate between self-assembled and surface-frozen monolayers, each dominated by one interaction. The phase behavior is rationalized within a thermodynamic model comprising interfacial interactions, elasticity, and entropic effects. Separating the substrate from the melt leaves the monolayer structurally intact.

Steric and chain length effects in the (√(3)×√(3))R30° structures of alkanethiol self-assembled monolayers on Au(111)

The translational and orientational potential energy surfaces (PESs) of n-alkanethiols with up to four carbon atoms are studied for (√(3)×√(3))R30° self-assembled monolayers (SAMs). The PESs indicate that methanethiol may form SAM structures that are not accessible for long-chain thiols. The tilt of the thiol molecules is determined by a compromise between the preferred binding geometry at the sulfur atom and the steric requirements of the alkane chains. The Au-S bond lengths, offset from the bridge position (brg), and the Au-S-C bond angles result in tilt angles of the S-C bond in the range of 55-60°. As DFT/generalized gradient approximation systematically underestimates chain-chain interactions, the binding energies are corrected by comparison to MP2 interaction energies of alkane dimers in SAM-like configurations. The resulting thiol binding energies increase by approximately 1 kcal mol(-1) per CH(2) group, which results in a substantial stabilization of long-chain SAMs due to chain-chain interactions. Furthermore, as the chain length increases, the accessible range of backbone tilt angles is constrained due to steric effects. The combination of these two effects may explain why SAM structures with long-chain thiols exhibit higher order in experiments. For each thiol two favorable SAM structures are found with the sulfur head group at the fcc-brg and hcp-brg positions, respectively. These domains may coexist in thermal equilibrium. In combination with the symmetry of the gold (111) surface, this raises the possibility of up to six different domains on single-crystal terraces. Reconstructions by an adatom or vacancy of ethanethiol SAMs with (√(3)×√(3))R30° lattice are also studied using PES scans. The results indicate that adsorption of thiols next to a vacancy is favorable and may lead to point defects inside SAMs.

Development of a semiempirical potential for simulations of thiol-gold interfaces. Application to thiol-protected gold nanoparticles

A new semiempirical potential, based on density functional calculations and a bond-order Morse-like potential, is developed to simulate the adsorption behavior of thiolate molecules on non-planar gold surfaces, including relaxing effects, in a more realistic way. The potential functions include as variables the metal-molecule separation, vibrational frequencies, bending and torsion angles between several pairs of atom types and the coordination number of both the metal (Au) and thiolate groups. The potential was parameterized based on a set of density functional calculations of molecular adsorption in several surface sites (i.e. hollow, bridge, top, on-top Au adatom and the novel staple motif) for different crystalline facets, i.e. Au(111) and (100). Langevin dynamics simulations have been performed to study the capping effects of alkanethiolates molecules on Au nanoparticles in the range 1-4 nm. The simulation results reveal an enhancement of the coverage degree whilst the nanoparticles diameter decreases. A high surface disorder due to the strong S-Au bond was found, in very good agreement with very recent experimental findings [M. M. Mariscal, J. A. Olmos-Asar, C. Gutierrez-Wing, A. Mayoral and M. J. Yacaman, Phys. Chem. Chem. Phys., 2010, 12, 11785].

Coverage-dependent formation of chiral ethylthiolate-Au complexes on Au(111)

We studied the coverage-dependent self-assembly of the flat-lying phase of ethylthiolate on Au(111). At low coverage, we observed the formation of short stripes of chiral Au-(SC(2)H(5))(2) complexes that arrange in a disordered phase. The latter grow partly at the expense of the native Au(111) surface reconstruction, which is fully lifted for a coverage of ∼0.60 ML. We found that the lift of the reconstruction and evaporation from step edges are competing adatom sources. Close to saturation coverage (0.70 to 0.75 ML), large, well-ordered domains with a (8 × √3)rectangular superstructure formed. Alternation of chirality was found in adjacent stripes as already reported for other short alkanethiolates. We suggest that, because of a simple geometrical consideration, the chirality should, on the contrary, be preserved in the stripe phase of longer alkanethiolates.

The complex thiol-palladium interface: a theoretical and experimental study

This paper presents a theoretical study of the surface structures and thermodynamic stability of different thiol and sulfide structures present on the palladium surface as a function of the chemical potential of the thiol species. It has been found that as the chemical potential of the thiol is increased, the initially clean palladium surface is covered by a (√3 × √3)R30° sulfur lattice. Further increase in the thiol pressure or concentration leads to the formation of a denser (√7 × √7)R19.1° sulfur lattice, which finally undergoes a phase transition to form a complex (√7 × √7)R19.1° sulfur + thiol adlayer (3/7 sulfur + 2/7 thiol coverage). This transition is accompanied by a strong reconstruction of the Pd(111) surface. The formation of these surface structures has been explained in terms of the catalytic properties of the palladium surface. These results have been compared with X-ray photoelectron spectroscopy results obtained for thiols adsorbed on different palladium surfaces.

On the atomic structure of thiol-protected gold nanoparticles: a combined experimental and theoretical study

In the present work new findings on the structure of the S-Au interface are presented. Theoretical calculations using a new semiempirical potential, based on density functional theory and a bond-order Morse potential, are employed to simulate the adsorption process in a more realistic way. The simulation results reveal the formation of gold adatoms on the nanoparticle surface and high surface disorder due to the strong S-Au bond. Experimental data were acquired by aberration (Cs) corrected scanning transmission electron microscopy (STEM) using a high angle annular dark field detector (HAADF) that showed a great similarity with the theory predicted.

Fluorescence correlation spectroscopy reveals strong fluorescence quenching of FITC adducts on PEGylated gold nanoparticles in water and the presence of fluorescent aggregates of desorbed thiolate ligands

Colloidal gold particles functionalised with oligoethylene-glycolated disulfide ligands and fluorescent moieties derived from fluorescein isothiocyanate (FITC) have been prepared and studied in aqueous suspension using fluorescence correlation spectroscopy (FCS). FCS probes the dynamics of the particles at the single object level, and reveals the desorption of fluorescent ligands which subsequently aggregate into larger (slower diffusing) objects. Cross-correlation spectroscopy of the FITC fluorescence and the Rayleigh-Mie scattering (RM-FCCS) of the gold cores shows that the only detectable fluorescent objects are free ligands and aggregates not associated with a gold particle. The fluorescence of bound fluorophores is quenched making their fluorescence too weak to be detected. FCS and RM-FCCS are useful tools for characterising functionalised noble metal particles in solution, under conditions similar to those used in optical bio-imaging. Desorption of thiolates from gold nanoparticles needs to be taken into account when working with these materials at low concentration.

Modeling the electronic properties of pi-conjugated self-assembled monolayers

The modification of electrode surfaces by depositing self-assembled monolayers (SAMs) provides the possibility for controlled adjustment of various key parameters in organic and molecular electronic devices. Most important among them are the work function of the electrode and the relative alignment of its Fermi level with the conducting states in the SAM itself and with those in a subsequently deposited organic semiconductor. For the efficient application of such interface modifications it is crucial to reach a proper understanding of the relation between the chemical structure of a molecule, its molecular electronic characteristics, and the properties of the SAM formed by such molecules. Over the past years, quantum-mechanical calculations have proven to be a valuable tool for reaching a fundamental understanding of the relevant structure-property relations. Here, we provide a review over the field and report on recent progress in the modeling of the interfacial electronic properties of pi-conjugated SAMs. In addition to the insight that can be gained from simple electrostatic considerations, we focus on the quantum-mechanical description of the roles played by substituents, molecular backbones, chemical anchoring groups, and the packing density of molecules on the surface. Furthermore, we explicitly address the energy-level alignment at the interface between a prototypical organic semiconductor and a SAM-covered metal electrode and describe an approach suitable for extending the metallic character of the substrate onto the monolayer.