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.

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.

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.

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.

Vacancy diffusion and coalescence in graphene directed by defect strain fields.

The formation of extended defects in graphene from the coalescence of individual mobile vacancies can significantly alter its mechanical, electrical and chemical properties. We present the results of ab initio simulations which demonstrate that the strain created by multi-vacancy complexes in graphene determine their overall growth morphology when formed from the coalescence of individual mobile lattice vacancies. Using density functional theory, we map out the potential energy surface for the motion of mono-vacancies in the vicinity of multi-vacancy defects. The inhomogeneous bond strain created by the multi-vacancy complexes strongly biases the activation energy barriers for single vacancy motion over a wide area. Kinetic Monte Carlo simulations based on rates from ab initio derived activation energies are performed to investigate the dynamical evolution of single vacancies in these strain fields. The resultant coalescence processes reveal that the dominant morphology of multi-vacancy complexes will consist of vacancy lines running in the two primary crystallographic directions, and that more thermodynamically stable structures, such as holes, are kinetically inaccessible from mono-vacancy aggregation alone.

Models of the interaction of metal tips with insulating surfaces.

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.

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.