Samuel Paul Jarvis

Mapping the force field of a hydrogen-bonded assembly

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy.

A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions.

Identifying passivated dynamic force microscopy tips on H:Si(100)

The chemical reactivity of the tip plays a central role in image formation in dynamic force microscopy, but in very many cases the state of the probe is a key experimental unknown. We show here that an H-terminated and thus chemically unreactive tip can be readily identified via characteristic imaging and spectroscopic (F(z)) signatures, including, in particular, contrast inversion, on hydrogen-passivated Si(100). We determine the tip apex termination by comparing site-specific difference force curves with the results of density functional theory, providing a clear protocol for the identification of chemically unreactive tips on silicon surfaces.

Measuring the mechanical properties of molecular conformers

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

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

Summary 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.

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 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 surface that negatively charged tips produce the best intramolecular contrast attributed to the enhancement of repulsive interactions.

Dewetting of Au nanoparticle assemblies

Atomic force microscopy measurements as a function of annealing temperature, time of exposure to a high relative humidity environment, and scan duration/parameters have been used to ascertain the stability of assemblies of thiol-passivated Au nanoparticles on silicon substrates. Striking changes in the morphology of self-organised nanoparticle patterns are observed following the exposure of samples to atmospheres with a relative humidity of 80%. The nanoparticle film dewets the underlying silicon substrate on exposure to water, forming locally thicker regions. Time-lapse imaging shows that the dewetting proceeds via layer-by-layer growth, and there is no evidence for classical coarsening mechanisms involving self-similar film morphologies. Annealing at temperatures between 100 °C and 160 °C produces a rather different dewetting effect for the highest temperatures and/or annealing times, where significant nanoparticle sintering promotes the break-up of the two-dimensional assembly. The morphology of the initial 2D film plays a key role in determining the time scale on which annealing promotes nanoparticle dewetting. Dewetting can also be induced by a scanning probe such that localised (micron-scale) areas of the nanoparticle assembly can be converted from 2D to 3D character.

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.

Complex design of dissipation signals in non-contact atomic force microscopy

Complex interplay between topography and dissipation signals in Non-Contact Atomic Force Microscopy (NC-AFM) is studied by a combination of state-of-the-art theory and experiment applied to the Si(001) surface prone to instabilities. Considering a wide range of tip-sample separations down to the near-contact regime and several tip models, both stiff and more flexible, a sophisticated architecture of hysteresis loops in the simulated tip force-distance curves is revealed. At small tip-surface distances the dissipation was found to be comprised of two related contributions due to both the surface and tip. These are accompanied by the corresponding surface and tip distortion approach-retraction dynamics. Qualitative conclusions drawn from the theoretical simulations such as large dissipation signals (>1.0 eV) and a step-like dissipation dependent on the tip-surface distance are broadly supported by the experimental observations. In view of the obtained results we also discuss the reproducibility of NC-AFM imaging.

Structural development and energy dissipation in simulated silicon apices

Summary 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.