Determination of in-plane surface directions in scanning probe microscopy images.

We describe an approach to determine the in-plane crystallographic surface directions in scanning probe microscopy (SPM) images. This method is based on a one-time characterization of the SPM instrument with an appropriate test sample and is exemplified by the analysis of non-contact atomic force microscopy (NC-AFM) images on surfaces whose natural cleavage occurs along {111} planes. We introduce a two-dimensional rotation matrix relating the crystallographic surface directions known from an analysis of the macroscopic crystal to the directions in the NC-AFM images. The procedure takes into account rotations and mirror axes resulting from sample mounting, the SPM scanner rotation, the choice of scan direction, as well as data processing, storage, and display. We demonstrate the practicability of the approach by determining the [112̄] direction in topographic images of a CeO2(111) film grown on a Si(111) wafer and atomic resolution images of CaF2(111) with an instrument based on the beetle-type scanner.

Water adsorption lifts the (2 × 1) reconstruction of calcite(104).

The adsorption of water on calcite(104) is investigated in ultra-high vacuum by density functional theory (DFT) and non-contact atomic force microscopy (NC-AFM) in the coverage regime of up to one monolayer (ML). DFT calculations reveal a clear preference for water to adsorb on the bulk-like carbonate group rows of the (2 × 1) reconstructed surface. Additionally, an apparent water attraction due to carbonate group reorientation suggest island formation for water adsorbed on the reconstructed carbonate group rows. Experimentally, water is found to exclusively occupy specific positions within the (2 × 1) unit cell up to 0.5 ML, to form islands at coverage between 0.5 and 1 ML, and to express a (1 × 1) structure at coverage of a full monolayer.

Differences in Molecular Adsorption Emanating from the (2 × 1) Reconstruction of Calcite(104).

Calcite, in the natural environment the most stable polymorph of calcium carbonate (CaCO3), not only is an abundant mineral in the Earth's crust but also forms a central constituent in the biominerals of living organisms. Intensive studies of calcite(104), the surface supporting virtually all processes, have been performed, and the interaction with a plethora of adsorbed species has been studied. Surprisingly, there is still serious ambiguity regarding the properties of the calcite(104) surface: effects such as a row-pairing or a (2 × 1) reconstruction have been reported, yet so far without physicochemical explanation. Here, we unravel the microscopic geometry of calcite(104) using high-resolution atomic force microscopy (AFM) data acquired at 5 K combined with density functional theory (DFT) and AFM image calculations. A (2 × 1) reconstruction of a pg-symmetric surface is found to be the thermodynamically most stable form. Most importantly, a decisive impact of the (2 × 1) reconstruction on adsorbed species is revealed for carbon monoxide.

Quantitative dynamic force microscopy with inclined tip oscillation.

In the mathematical description of dynamic atomic force microscopy (AFM), the relation between the tip-surface normal interaction force, the measurement observables, and the probe excitation parameters is defined by an average of the normal force along the sampling path over the oscillation cycle. Usually, it is tacitly assumed that tip oscillation and force data recording follows the same path perpendicular to the surface. Experimentally, however, the sampling path representing the tip oscillating trajectory is often inclined with respect to the surface normal and the data recording path. Here, we extend the mathematical description of dynamic AFM to include the case of an inclined sampling path. We find that the inclination of the tip movement can have critical consequences for data interpretation, especially for measurements on nanostructured surfaces exhibiting significant lateral force components. Inclination effects are illustrated by simulation results that resemble the representative experimental conditions of measuring a heterogeneous atomic surface. We propose to measure the AFM observables along a path parallel to the oscillation direction in order to reliably recover the force along this direction.

Double sample holder for efficient high-resolution studies of an insulator and a metal surface.

A double sample holder supporting both a metal sample and an insulator crystal for high-resolution scanning probe microscopy experiments is described. The metal sample serves as a substrate for tip preparation and tip functionalization to efficiently and reliably enable high-resolution studies of the adjacent insulator surface. Imaging of Ag(111)/mica, Au(111)/mica, CaF2(111), and calcite(104) surfaces is demonstrated at 5 K, including images on calcite(104) produced with a CO terminated tip, which was prepared on the adjacent metal sample.

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.

CO adsorption on the calcite(10.4) surface: a combined experimental and theoretical study.

Detailed information on structural, chemical, and physical properties of natural cleaved (10.4) calcite surfaces was obtained by a combined atomic force microscopy (AFM) and infrared (IR) study using CO as a probe molecule under ultrahigh vacuum (UHV) conditions. The structural quality of the surfaces was determined using non-contact AFM (NC-AFM), which also allowed assigning the adsorption site of CO molecules. Vibrational frequencies of adsorbed CO species were determined by polarization-resolved infrared reflection absorption spectroscopy (IRRAS). At low exposures, adsorption of CO on the freshly cleaved (10.4) calcite surface at a temperature of 62 K led to the occurrence of a single C-O vibrational band located at 2175.8 cm-1, blue-shifted with respect to the gas phase value. For larger exposures, a slight, coverage-induced redshift was observed, leading to a frequency of 2173.4 cm-1 for a full monolayer. The width of the vibrational bands is extremely small, providing strong evidence that the cleaved calcite surface is well-defined with only one CO adsorption site. A quantitative analysis of the IRRA spectra recorded at different surface temperatures revealed a CO binding energy of -0.31 eV. NC-AFM data acquired at 5 K for sub-monolayer CO coverage reveal single molecules imaged as depressions at the position of the protruding surface features, in agreement with the IRRAS results. Since there are no previous experimental data of this type, the interpretation of the results was aided by employing density functional theory calculations to determine adsorption geometries, binding energies, and vibrational frequencies of carbon monoxide on the (10.4) calcite surface. It was found that the preferred geometry of CO on this surface is adsorption on top of calcium in a slightly tilted orientation. With increased coverage, the binding energy shows a small decrease, revealing the presence of repulsive adsorbate-adsorbate interactions.

PTCDA adsorption on CaF2 thin films.

Thin insulating films are commonly employed for the electronic decoupling of molecules as they enable a preservation of the intrinsic molecular electronic functionality. Here, the molecular properties of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) adsorbed on insulating CaF2 thin films that were grown on Si(111) surfaces are studied. Scanning tunnelling microscopy is used to compare the properties of PTCDA molecules adsorbed on a partly CaF1-covered Si(111) surface with deposition on thicker CaF2/CaF1/Si(111) films. The identification of mostly single molecules on the CaF1/Si(111) interface layer is explained by the presence of atomic-size defects within this layer. Geometry-optimisation calculations using density functional theory reveal a geometry on CaF2(111) of nearly flat-lying PTCDA molecules with two oxygen atoms displaced towards calcium surface ions. This geometry is in agreement with the experimental observations.

Protruding hydrogen atoms as markers for the molecular orientation of a metallocene.

A distinct dumbbell shape is observed as the dominant contrast feature in the experimental data when imaging 1,1'-ferrocene dicarboxylic acid (FDCA) molecules on bulk and thin film CaF2(111) surfaces with non-contact atomic force microscopy (NC-AFM). We use NC-AFM image calculations with the probe particle model to interpret this distinct shape by repulsive interactions between the NC-AFM tip and the top hydrogen atoms of the cyclopentadienyl (Cp) rings. Simulated NC-AFM images show an excellent agreement with experimental constant-height NC-AFM data of FDCA molecules at several tip-sample distances. By measuring this distinct dumbbell shape together with the molecular orientation, a strategy is proposed to determine the conformation of the ferrocene moiety, herein on CaF2(111) surfaces, by using the protruding hydrogen atoms as markers.

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.

Growth kinetics of racemic heptahelicene-2-carboxylic acid nanowires on calcite (104).

Molecular self-assembly of racemic heptahelicene-2-carboxylic acid on a dielectric substrate at room temperature can be used to generate wire-like organic nanostructures consisting of single and double molecular rows. By means of non-contact atomic force microscopy, we investigate the growth of the wire-like pattern after deposition by experimental and theoretical means. From analyzing the time dependence of the mean row length, two distinct regimes were found. At the early post-deposition stage, the mean length grows in time. Subsequently, a crossover to a second regime is observed, where the mean row length remains nearly constant. We explain these findings by a mean-field rate equation approach providing a comprehensive picture of the growth kinetics. As a result, we demonstrate that the crossover between the two distinct regimes is accomplished by vanishing of the homochiral single rows. At later stages only heterochiral double row structures remain.

Organisation and ordering of 1D porphyrin polymers synthesised by on-surface Glaser coupling.

One-dimensional polymer chains consisting of π-conjugated porphyrin units are formed via Glaser coupling on a Ag(111) surface. Scanning probe microscopy reveals the covalent structure of the products and their ordering. The conformational flexibility within the chains is investigated via a comparision of room temperature and cryogenic measurements.

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.

Consecutive Charging of a Molecule-on-Insulator Ensemble Using Single Electron Tunnelling Methods.

We present the local charge state modification at room temperature of small insulator-supported molecular ensembles formed by 1,1'-ferrocenedicarboxylic acid on calcite. Single electron tunnelling between the conducting tip of a noncontact atomic force microscope (NC-AFM) and the molecular islands is observed. By joining NC-AFM with Kelvin probe force microscopy, successive charge build-up in the sample is observed from consecutive experiments. Charge transfer within the islands and structural relaxation of the adsorbate/surface system is suggested by the experimental data.

Noise in NC-AFM measurements with significant tip-sample interaction.

The frequency shift noise in non-contact atomic force microscopy (NC-AFM) imaging and spectroscopy consists of thermal noise and detection system noise with an additional contribution from amplitude noise if there are significant tip-sample interactions. The total noise power spectral density DΔf (fm) is, however, not just the sum of these noise contributions. Instead its magnitude and spectral characteristics are determined by the strongly non-linear tip-sample interaction, by the coupling between the amplitude and tip-sample distance control loops of the NC-AFM system as well as by the characteristics of the phase locked loop (PLL) detector used for frequency demodulation. Here, we measure DΔf (fm) for various NC-AFM parameter settings representing realistic measurement conditions and compare experimental data to simulations based on a model of the NC-AFM system that includes the tip-sample interaction. The good agreement between predicted and measured noise spectra confirms that the model covers the relevant noise contributions and interactions. Results yield a general understanding of noise generation and propagation in the NC-AFM and provide a quantitative prediction of noise for given experimental parameters. We derive strategies for noise-optimised imaging and spectroscopy and outline a full optimisation procedure for the instrumentation and control loops.

Frequency-modulated atomic force microscopy operation by imaging at the frequency shift minimum: the dip-df mode.

In frequency modulated non-contact atomic force microscopy, the change of the cantilever frequency (Δf) is used as the input signal for the topography feedback loop. Around the Δf(z) minimum, however, stable feedback operation is challenging using a standard proportional-integral-derivative (PID) feedback design due to the change of sign in the slope. When operated under liquid conditions, it is furthermore difficult to address the attractive interaction regime due to its often moderate peakedness. Additionally, the Δf signal level changes severely with time in this environment due to drift of the cantilever frequency f0 and, thus, requires constant adjustment. Here, we present an approach overcoming these obstacles by using the derivative of Δf with respect to z as the input signal for the topography feedback loop. Rather than regulating the absolute value to a preset setpoint, the slope of the Δf with respect to z is regulated to zero. This new measurement mode not only makes the minimum of the Δf(z) curve directly accessible, but it also benefits from greatly increased operation stability due to its immunity against f0 drift. We present isosurfaces of the Δf minimum acquired on the calcite CaCO3(101̅4) surface in liquid environment, demonstrating the capability of our method to image in the attractive tip-sample interaction regime.

Substrate templating guides the photoinduced reaction of C60 on calcite.

A substrate-guided photochemical reaction of C60 fullerenes on calcite, a bulk insulator, investigated by non-contact atomic force microscopy is presented. The success of the covalent linkage is evident from a shortening of the intermolecular distances, which is clearly expressed by the disappearance of the moiré pattern. Furthermore, UV/Vis spectroscopy and mass spectrometry measurements carried out on thick films demonstrate the ability of our setup for initiating the photoinduced reaction. The irradiation of C60 results in well-oriented covalently linked domains. The orientation of these domains is dictated by the lattice dimensions of the underlying calcite substrate. Using the lattice mismatch to deliberately steer the direction of the chemical reaction is expected to constitute a general design principle for on-surface synthesis. This work thus provides a strategy for controlled fabrication of oriented, covalent networks on bulk insulators.

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.

Tuning molecular self-assembly on bulk insulator surfaces by anchoring of the organic building blocks.

Molecular self-assembly constitutes a versatile strategy for creating functional structures on surfaces. Tuning the subtle balance between intermolecular and molecule-surface interactions allows structure formation to be tailored at the single-molecule level. While metal surfaces usually exhibit interaction strengths in an energy range that favors molecular self-assembly, dielectric surfaces having low surface energies often lack sufficient interactions with adsorbed molecules. As a consequence, application-relevant, bulk insulating materials pose significant challenges when considering them as supporting substrates for molecular self-assembly. Here, the current status of molecular self-assembly on surfaces of wide-bandgap dielectric crystals, investigated under ultrahigh vacuum conditions at room temperature, is reviewed. To address the major issues currently limiting the applicability of molecular self-assembly principles in the case of dielectric surfaces, a systematic discussion of general strategies is provided for anchoring organic molecules to bulk insulating materials.

Controlling molecular self-assembly on an insulating surface by rationally designing an efficient anchor functionality that maintains structural flexibility.

Molecular self-assembly on surfaces is dictated by the delicate balance between intermolecular and molecule-surface interactions. For many insulating surfaces, however, the molecule-surface interactions are weak and rather unspecific. Enhancing these interactions, on the other hand, often puts a severe limit on the achievable structural variety. To grasp the full potential of molecular self-assembly on these application-relevant substrates, therefore, requires strategies for anchoring the molecular building blocks toward the surface in a way that maintains flexibility in terms of intermolecular interaction and relative molecule orientation. Here, we report the design of a site-specific anchor functionality that provides strong anchoring toward the surface, resulting in a well-defined adsorption position. At the same time, the anchor does not significantly interfere with the intermolecular interaction, ensuring structural flexibility. We demonstrate the success of this approach with three molecules from the class of shape-persistent oligo(p-benzamide)s adsorbed onto the calcite(10.4) surface. These molecules have the same aromatic backbone with iodine substituents, providing the same basic adsorption mechanism to the surface calcium cations. The backbone is equipped with different functional groups. These have a negligible influence on the molecular adsorption on the surface but significantly change the intermolecular interaction. We show that distinctly different molecular structures are obtained that wet the surface due to the strong linker while maintaining variability in the relative molecular orientation. With this study, we thus provide a versatile strategy for increasing the structural richness in molecular self-assembly on insulating substrates.