Cyclic Single Atom Vertical Manipulation on a Nonmetallic Surface.

Motivated by the quest for experimental procedures capable of controlled manipulation of single atoms on surfaces, we set up a computational strategy that explores the cyclical vertical manipulation of a broad set of single atoms on the GaAs(110) surface. First-principles simulations of atomic force microscope tip-sample interactions were performed considering families of GaAs and Au-terminated tip apexes with varying crystalline termination. We identified a subset of tips capable of both picking up and depositing an adatom (Ga, As, Al, and Au) any number of times via a modify-restore cycle that "resets" the apex of the scanning probe to its original structure at the end of each cycle. Manipulation becomes successful within a certain window of lateral and vertical tip distances that are observed to be different for extracting and depositing each atom. A practical experimental protocol of special utility for potential cyclical manipulation of single atoms on a nonmetallic surface is proposed.

Chemical shielding of H2O and HF encapsulated inside a C60 cage.

Molecular surgery provides the opportunity to study relatively large molecules encapsulated within a fullerene cage. Here we determine the location of an H2O molecule isolated within an adsorbed buckminsterfullerene cage, and compare this to the intrafullerene position of HF. Using normal incidence X-ray standing wave (NIXSW) analysis, coupled with density functional theory and molecular dynamics simulations, we show that both H2O and HF are located at an off-centre position within the fullerene cage, caused by substantial intra-cage electrostatic fields generated by surface adsorption of the fullerene. The atomistic and electronic structure simulations also reveal significant internal rotational motion consistent with the NIXSW data. Despite this substantial intra-cage interaction, we find that neither HF or H2O contribute to the endofullerene frontier orbitals, confirming the chemical isolation of the encapsulated molecules. We also show that our experimental NIXSW measurements and theoretical data are best described by a mixed adsorption site model.

Automated Searching and Identification of Self-Organized Nanostructures.

Currently, researchers spend significant time manually searching through large volumes of data produced during scanning probe imaging to identify specific patterns and motifs formed via self-assembly and self-organization. Here, we use a combination of Monte Carlo simulations, general statistics, and machine learning to automatically distinguish several spatially correlated patterns in a mixed, highly varied data set of real AFM images of self-organized nanoparticles. We do this regardless of feature-scale and without the need for manually labeled training data. Provided that the structures of interest can be simulated, the strategy and protocols we describe can be easily adapted to other self-organized systems and data sets.

Automated extraction of single H atoms with STM: tip state dependency.

The atomistic structure of the tip apex plays a crucial role in performing reliable atomic-scale surface and adsorbate manipulation using scanning probe techniques. We have developed an automated extraction routine for controlled removal of single hydrogen atoms from the H:Si(100) surface. The set of atomic extraction protocols detect a variety of desorption events during scanning tunneling microscope (STM)-induced modification of the hydrogen-passivated surface. The influence of the tip state on the probability for hydrogen removal was examined by comparing the desorption efficiency for various classifications of STM topographs (rows, dimers, atoms, etc). We find that dimer-row-resolving tip apices extract hydrogen atoms most readily and reliably (and with least spurious desorption), while tip states which provide atomic resolution counter-intuitively have a lower probability for single H atom removal.

Visualizing the orientational dependence of an intermolecular potential.

Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard-Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation.

Nano-contact microscopy of supracrystals.

BACKGROUND: Highly ordered three-dimensional colloidal crystals (supracrystals) comprised of 7.4 nm diameter Au nanocrystals (with a 5% size dispersion) have been imaged and analysed using a combination of scanning tunnelling microscopy and dynamic force microscopy. RESULTS: By exploring the evolution of both the force and tunnel current with respect to tip-sample separation, we arrive at the surprising finding that single nanocrystal resolution is readily obtained in tunnelling microscopy images acquired more than 1 nm into the repulsive (i.e., positive force) regime of the probe-nanocrystal interaction potential. Constant height force microscopy has been used to map tip-sample interactions in this regime, revealing inhomogeneities which arise from the convolution of the tip structure with the ligand distribution at the nanocrystal surface. CONCLUSION: Our combined STM-AFM measurements show that the contrast mechanism underpinning high resolution imaging of nanoparticle supracrystals involves a form of nanoscale contact imaging, rather than the through-vacuum tunnelling which underpins traditional tunnelling microscopy and spectroscopy.

Critical assessment of the evidence for striped nanoparticles.

There is now a significant body of literature which reports that stripes form in the ligand shell of suitably functionalised Au nanoparticles. This stripe morphology has been proposed to strongly affect the physicochemical and biochemical properties of the particles. We critique the published evidence for striped nanoparticles in detail, with a particular focus on the interpretation of scanning tunnelling microscopy (STM) data (as this is the only technique which ostensibly provides direct evidence for the presence of stripes). Through a combination of an exhaustive re-analysis of the original data, in addition to new experimental measurements of a simple control sample comprising entirely unfunctionalised particles, we show that all of the STM evidence for striped nanoparticles published to date can instead be explained by a combination of well-known instrumental artefacts, or by issues with data acquisition/analysis protocols. We also critically re-examine the evidence for the presence of ligand stripes which has been claimed to have been found from transmission electron microscopy, nuclear magnetic resonance spectroscopy, small angle neutron scattering experiments, and computer simulations. Although these data can indeed be interpreted in terms of stripe formation, we show that the reported results can alternatively be explained as arising from a combination of instrumental artefacts and inadequate data analysis techniques.

Identifying tips for intramolecular NC-AFM imaging via in situ fingerprinting.

A practical experimental strategy is proposed that could potentially enable greater control of the tip apex in non-contact atomic force microscopy experiments. It is based on a preparation of a structure of interest alongside a reference surface reconstruction on the same sample. Our proposed strategy is as follows. Spectroscopy measurements are first performed on the reference surface to identify the tip apex structure using a previously collected database of responses of different tips to this surface. Next, immediately following the tip identification protocol, the surface of interest is studied (imaging, manipulation and/or spectroscopy). The prototype system we choose is the mixed Si(111)-7×7 and Ag:Si(111)-(√3 × âˆš3) R30° surface which can be prepared on the same sample with a controlled ratio of reactive and passivated regions. Using an "in silico" approach based on ab initio density functional calculations and a set of tips with varying chemical reactivities, we show how one can perform tip fingerprinting using the Si(111)-7×7 reference surface. Then it is found by examining the imaging of a naphthalene tetracarboxylic diimide (NTCDI) molecule adsorbed on Ag:Si(111)-(√3 × âˆš3) R30° surface that negatively charged tips produce the best intramolecular contrast attributed to the enhancement of repulsive interactions.

Unique determination of "subatomic" contrast by imaging covalent backbonding.

The origin of so-called "subatomic" resolution in dynamic force microscopy has remained controversial since its first observation in 2000. A number of detailed experimental and theoretical studies have identified different possible physicochemical mechanisms potentially giving rise to subatomic contrast. In this study, for the first time we are able to assign the origin of a specific instance of subatomic contrast as being due to the back bonding of a surface atom in the tip-sample junction.

Scanning probe image wizard: a toolbox for automated scanning probe microscopy data analysis.

We describe SPIW (scanning probe image wizard), a new image processing toolbox for SPM (scanning probe microscope) images. SPIW can be used to automate many aspects of SPM data analysis, even for images with surface contamination and step edges present. Specialised routines are available for images with atomic or molecular resolution to improve image visualisation and generate statistical data on surface structure.

Structural development and energy dissipation in simulated silicon apices.

In this paper we examine the stability of silicon tip apices by using density functional theory (DFT) calculations. We find that some tip structures - modelled as small, simple clusters - show variations in stability during manipulation dependent on their orientation with respect to the sample surface. Moreover, we observe that unstable structures can be revealed by a characteristic hysteretic behaviour present in the F(z) curves that were calculated with DFT, which corresponds to a tip-induced dissipation of hundreds of millielectronvolts resulting from reversible structural deformations. Additionally, in order to model the structural evolution of the tip apex within a low temperature NC-AFM experiment, we simulated a repeated tip-surface indentation until the tip structure converged to a stable termination and the characteristic hysteretic behaviour was no longer observed. Our calculations suggest that varying just a single rotational degree of freedom can have as measurable an impact on the tip-surface interaction as a completely different tip structure.

Combining nanoscale manipulation with macroscale relocation of single quantum dots.

We have controllably positioned, with nanometre precision, single CdSe quantum dots referenced to a registration template such that the location of a given nanoparticle on a macroscopic (≈1 cm(2)) sample surface can be repeatedly revisited. The atomically flat sapphire substrate we use is particularly suited to optical measurements of the isolated quantum dots, enabling combined manipulation-spectroscopy experiments on a single particle. Automated nanoparticle manipulation and imaging routines have been developed so as to facilitate the rapid assembly of specific nanoparticle arrangements.

Mono- and multi-layer adsorption of an ionic liquid on Au(110).

Ultraviolet photoelectron spectroscopy (UPS), work function measurements, low energy electron diffraction (LEED) and scanning tunnelling microscopy (STM) have been used to study the adsorption and desorption of 1-ethyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, [C(2)C(1)Im][Tf(2)N], on the (1×2) clean surface reconstruction of Au(110) in the temperature range 100-674 K. The ionic liquid adsorbed without decomposition, and desorbed without leaving any residue on the surface. For adsorption at room temperature a monolayer of strongly bound ionic liquid was formed with four interface states visible in UP spectra. STM at 100 K showed that the monolayer consisted of well-ordered rows of adsorbed ionic liquid aligned parallel to the close packed rows of surface gold atoms (the [110] direction) with a separation of ×2 (the same as the clean surface reconstruction) between the rows in the orthogonal [001] direction. Multilayer adsorption at room temperature occurred by droplet formation followed by smoothing of the droplets to a layered morphology with time. Heating caused multilayer desorption at temperatures in the 363-383 K range, followed by partial monolayer desorption at 548 K to produce a Au(110)-(1×3) reconstructed surface with sub-monolayer domains of ionic liquid. Desorption of the remaining ionic liquid at 600 K caused the gold surface to reconstruct back to the clean (1×2) reconstruction.

Effect of the tip state during qPlus noncontact atomic force microscopy of Si(100) at 5 K: Probing the probe.

BACKGROUND: Noncontact atomic force microscopy (NC-AFM) now regularly produces atomic-resolution images on a wide range of surfaces, and has demonstrated the capability for atomic manipulation solely using chemical forces. Nonetheless, the role of the tip apex in both imaging and manipulation remains poorly understood and is an active area of research both experimentally and theoretically. Recent work employing specially functionalised tips has provided additional impetus to elucidating the role of the tip apex in the observed contrast. RESULTS: We present an analysis of the influence of the tip apex during imaging of the Si(100) substrate in ultra-high vacuum (UHV) at 5 K using a qPlus sensor for noncontact atomic force microscopy (NC-AFM). Data demonstrating stable imaging with a range of tip apexes, each with a characteristic imaging signature, have been acquired. By imaging at close to zero applied bias we eliminate the influence of tunnel current on the force between tip and surface, and also the tunnel-current-induced excitation of silicon dimers, which is a key issue in scanning probe studies of Si(100). CONCLUSION: A wide range of novel imaging mechanisms are demonstrated on the Si(100) surface, which can only be explained by variations in the precise structural configuration at the apex of the tip. Such images provide a valuable resource for theoreticians working on the development of realistic tip structures for NC-AFM simulations. Force spectroscopy measurements show that the tip termination critically affects both the short-range force and dissipated energy.

Measuring Si-C60 chemical forces via single molecule spectroscopy.

We measure the short-range chemical force between a silicon-terminated tip and individual adsorbed C(60) molecules using frequency modulation atomic force microscopy. The interaction with an adsorbed fullerene is sufficiently strong to drive significant atomic rearrangement of tip structures.

Toggling bistable atoms via mechanical switching of bond angle.

We reversibly switch the state of a bistable atom by direct mechanical manipulation of bond angle using a dynamic force microscope. Individual buckled dimers at the Si(100) surface are flipped via the formation of a single covalent bond, actuating the smallest conceivable in-plane toggle switch (two atoms) via chemical force alone. The response of a given dimer to a flip event depends critically on both the local and nonlocal environment of the target atom-an important consideration for future atomic scale fabrication strategies.

Directing the formation of nanostructured rings via local oxidation.

We provide compelling evidence that ring formation in solutions of thiol-passivated Au nanoparticles is driven by breath figure dynamics. A method for the controlled placement of rings of nanoparticles on a solid substrate, which exploits variations in substrate wettability to fix the positions of the submicrometer water droplets formed in the breath figure process, has been developed. This is achieved by heterogeneously patterning hydrogen-terminated silicon substrates with oxide regions that act as adsorption sites for the droplets. The droplets in turn template the formation of thiol-passivated Au nanoparticle rings during spin-casting from volatile solvents.