Thomas Trevethan

Functionalized Truxenes: Adsorption and Diffusion of Single Molecules on the KBr(001) Surface

In this work, we have studied the adsorption and diffusion of large functionalized organic molecules on an insulating ionic surface at room temperature using a noncontact atomic force microscope (NC-AFM) and theoretical modeling. Custom designed syn-5,10,15-tris(4-cyanophenylmethyl)truxene molecules are adsorbed onto the nanoscale structured KBr(001) surface at low coverages and imaged with atomic and molecular resolution with the NC-AFM. The molecules are observed rapidly diffusing along the perfect monolayer step edges and immobilized at monolayer kink sites. Extensive atomistic simulations elucidate the mechanisms of adsorption and diffusion of the molecule on the different surface features. The results of this study suggest methods of controlling the diffusion of adsorbates on insulating and nanostructured surfaces.

Unambiguous Determination of the Adsorption Geometry of a Metal—Organic Complex on a Bulk Insulator

Individual molecules of Co-Salen, a small chiral paramagnetic metal--organic Schiff base complex, were deposited on NaCl(001) and subsequently imaged with noncontact atomic force microscopy employing Cr coated tips in a cryogenic ultrahigh vacuum environment. Images were obtained in which both the position and orientation of the adsorbed molecules and the atomic structure of the surface are resolved simultaneously, enabling the determination of the exact adsorption site. Density functional theory calculations were used to identify the ionic sublattice resolved with the Cr tip and also to confirm the adsorption site and orientation of the molecule on the surface. These calculations show that the central Co atom of the molecule physisorbs on top of a Cl ion and is aligned along 110-directions in its lowest energy configuration. In addition, a local energy minimum exists along 100-directions. Due to the chirality of the molecule, two mirror symmetric configurations rotated by approximately +/-5 degrees away from these directions are energetically equivalent. The resulting 16 low energy configurations are observed in the experimental images.

On the validity of empirical potentials for simulating radiation damage in graphite: a benchmark

In this work, the ability of methods based on empirical potentials to simulate the effects of radiation damage in graphite is examined by comparing results for point defects, found using ab initio calculations based on density functional theory (DFT), with those given by two state of the art potentials: the Environment-Dependent Interatomic Potential (EDIP) and the Adaptive Intermolecular Reactive Empirical Bond Order potential (AIREBO). Formation energies for the interstitial, the vacancy and the Stone-Wales (5775) defect are all reasonably close to DFT values. Both EDIP and AIREBO can thus be suitable for the prompt defects in a cascade, for example. Both potentials suffer from arefacts. One is the pinch defect, where two α-atoms adopt a fourfold-coordinated sp(3) configuration, that forms a cross-link between neighbouring graphene sheets. Another, for AIREBO only, is that its ground state vacancy structure is close to the transition state found by DFT for migration. The EDIP fails to reproduce the ground state self-interstitial structure given by DFT, but has nearly the same formation energy. Also, for both potentials, the energy barriers that control diffusion and the evolution of a damage cascade, are not well reproduced. In particular the EDIP gives a barrier to removal of the Stone-Wales defect as 0.9 eV against DFTs 4.5 eV. The suite of defect structures used is provided as supplementary information as a benchmark set for future potentials.

Is atomic-scale dissipation in NC-AFM real? Investigation using virtual atomic force microscopy

Using a virtual dynamic atomic force microscope, that explicitly simulates the operation of a non-contact AFM experiment, we have performed calculations to investigate the formation of atomic-scale contrast in dissipation images. A non-conservative tip?surface interaction was implemented using the theory of dynamical response in scanning probe microscopy with energies and barriers derived from realistic atomistic modelling. It is shown how contrast in the damping signal is due to the hysteresis in the tip?surface force and not an artefact of the finite response of the complicated instrumentation. Topography and dissipation images of the CaO(001) surface are produced which show atomic-scale contrast in the dissipation with a corrugation of approximately 0.1?eV, which is typical of that observed in images of similar binary ionic surfaces. The effect of the fast-direction scanning speed on the image formation is also investigated and discussed.

Organic Molecules Reconstruct Nanostructures on Ionic Surfaces

Modification and functionalization of the atomic-scale structure of insulating surfaces is fundamental to catalysis, self-assembly, and single-molecule technologies. Specially designed syn-5,10,15-tris(4-cyanophenylmethyl)truxene molecules can reshape features on an ionic KBr (001) surface. Atomic force microscopy images demonstrate that both KBr monolayer islands and pits can reshape from rectangular to round structures, a process which is directly facilitated by molecular adsorption. Simulations reveal that the mechanism of the surface reconstruction consists of collective atomic hops of ions on the step edges of the islands and pits, which correlate with molecular motion. The energy barriers for individual processes are reduced by the presence of the adsorbed molecules, which cause surface structural changes. These results show how appropriately designed organic molecules can modify surface morphology on insulating surfaces. Such strongly adsorbed molecules can also serve as anchoring sites for building new nanostructures on inert insulating surfaces.

Modelling atomic scale manipulation with the non-contact atomic force microscope

We present the results of calculations performed to model the process of lateral manipulation of an oxygen vacancy in the MgO(001) surface using the non-contact atomic force microscope (NC-AFM). The potential energy surfaces for the manipulation as a function of tip position are determined from atomistic modelling of the MgO(001) surface interacting with a Mg terminated MgO tip. These energies are then used to model the dynamical evolution of the system as the tip oscillates and at a finite temperature using a kinetic Monte Carlo method. The manipulation process is strongly dependent on the lateral position of the tip and the system temperature. It is also found that the expectation value of the point at which the vacancy jumps depends on the trajectory of the oscillating cantilever as the surface is approached. The effect of the manipulation on the operation of the NC-AFM is modelled with a virtual dynamic AFM, which explicitly simulates the entire experimental instrumentation and control loops. We show how measurable experimental signals can result from a single controlled atomic scale event and suggest the most favourable conditions for achieving successful atomic scale manipulation experimentally.

Controlling electron transfer processes on insulating surfaces with the non-contact atomic force microscope.

We present the results of theoretical modelling that predicts how a process of transfer of single electrons between two defects on an insulating surface can be induced using a scanning force microscope tip. A model but realistic system is employed which consists of a neutral oxygen vacancy and a noble metal (Pt or Pd) adatom on the MgO(001) surface. We show that the ionization potential of the vacancy and the electron affinity of the metal adatom can be significantly modified by the electric field produced by an ionic tip apex at close approach to the surface. The relative energies of the two states are also a function of the separation of the two defects. Therefore the transfer of an electron from the vacancy to the metal adatom can be induced either by the field effect of the tip or by manipulating the position of the metal adatom on the surface.

Modelling components of future molecular devices

We discuss challenges involved in modelling different components of molecular devices and give several examples that demonstrate how computer modelling evolved over the last few years to become a comprehensive tool for designing molecules, predicting their adsorption and diffusion at surfaces, simulating atomic force microscopy imaging and manipulation of atoms and molecules at insulating surfaces and studying electron conduction in prototype molecular devices. We describe some of the computational techniques used for modelling adsorption, diffusion, imaging and manipulation of organic molecules at surfaces and challenges pertaining to these studies, give several examples of applications and discuss further prospects for theoretical modelling of complex organic molecules at surfaces.

Models of the interaction of metal tips with insulating surfaces

Summary We present the results of atomistic simulations of metallic atomic-force-microscopy tips interacting with ionic substrates, with atomic resolution. Chromium and tungsten tips are used to image the NaCl(001) and MgO(001) surfaces. The interaction of the tips with the surface is simulated by using density-functional-theory calculations employing a mixed Gaussian and plane-wave basis and cluster-tip models. In each case, the apex of the metal cluster interacts more attractively with anions in the surfaces than with cations, over the range of typical imaging distances, which leads to these sites being imaged as raised features (bright) in constant-frequency-shift images. We compare the results of the interaction of a chromium tip with the NaCl surface, with calculations employing exclusively plane-wave basis sets and a fully periodic tip model, and demonstrate that the electronic structure of the tip model employed can have a significant quantitative effect on calculated forces when the tip and surface are clearly separated.

A comparison of dynamic atomic force microscope set-ups for performing atomic scale manipulation experiments

We present the results of calculations performed to investigate the process of single-atom manipulation with the non-contact atomic force microscope comparing the two most common experimental set-ups: a conventional large amplitude silicon cantilever and a small amplitude quartz tuning fork. The manipulation of a model system-an oxygen vacancy in the MgO(001) surface by a single vertical approach at a fixed lateral position-is simulated for each set-up using a detailed and realistic atomistic model that accounts for temperature and the tip trajectory, and it is found that both approaches produce the manipulation event in approximately the same way. The behaviour of the tip dynamics and the resulting response of the instrumentation to the manipulation event is studied using a virtual dynamic atomic force microscope that includes a realistic description of noise for each type of set-up. The results of these calculations indicate how a single-atom manipulation can be performed and recognized by each type of experiment.