Complex Surface Diffusion Mechanisms of Cobalt Phthalocyanine Molecules on Ag(100).

We used time-lapsed scanning tunneling microscopy between 43 and 50 K and density functional theory (DFT) to explore the basic surface diffusion steps of cobalt phthalocyanine (CoPc) molecules on the Ag(100) surface. We show that the CoPc molecules translate and rotate on the surface in the same temperature range. Both processes are associated with similar activation energies; however, the translation is more frequently observed. Our DFT calculations provide the activation energies for the translation of the CoPc molecule between the nearest hollow sites and the rotation at both the hollow and the bridge sites. The activation energies are only consistent with the experimental findings, if the surface diffusion mechanism involves a combined translational and rotational molecular motion. Additionally, two channels of motion are identified: the first provides only a channel for translation, while the second provides a channel for both the translation and the rotation. The existence of the two channels explains a higher rate for the translation determined in experiment.

Room temperature discrimination of adsorbed molecules and attachment sites on the Si(111)-7 × 7 surface using a qPlus sensor.

In this paper, we show that simultaneous noncontact atomic force microscopy (nc-AFM) and scanning tunneling microscopy (STM) is a powerful tool for molecular discrimination on the Si(111)-7 × 7 surface, even at room temperature. Using density functional theory modeling, we justify this approach and show that the force response allows us to distinguish straightforwardly between molecular adsorbates and common defects, such as vacancies. Finally, we prove that STM/nc-AFM method is able to determine attachment sites of molecules deposited on semiconductor surface at room temperature.

Understanding dissipative tip-molecule interactions with submolecular resolution on an organic adsorbate.

Three-dimensional force spectroscopy measurements on 3,4,9,10-perylene-tetra-carboxylic dianhydride adsorbed on Ag(111) are combined with first-principles calculations to characterize the dissipative tip-molecule interactions with submolecular resolution. The experiments reveal systematic differences between the energy dissipation at the end groups and the center of the molecules that change with the tip-sample distance. Guided by the strength of the experimental conservative forces, an Ag-contaminated Si tip is identified as the likely tip termination in the experiments. Based on this tip configuration, the energy dissipation in the tip-sample contact is determined from the approach and retraction force curves calculated as a function of distance for different molecule sites. These calculations provide an explanation for the experimental trends in terms of the competition between localized dissipation mechanisms involving the quite mobile oxygen atoms on the sides of the molecule, and global molecular deformations involving the more rigid perylene core. The results confirm that the observed dissipation can be explained in terms of adhesion hysteresis and show the power of combined experimental-theoretical spectroscopy studies in the characterization of the underlying microscopic mechanisms.

Theoretical study of electronic and transport properties of PPy-Pt(111) and PPy-C(111):H interfaces.

We present a first-principles study of promising hybrid organic-inorganic interface systems consisting of a polypyrrole (PPy) chain sandwiched between metallic Pt(111) or hydrogen-terminated diamond C(111):H electrodes. We combine ab initio density-functional-theory total energy calculations, Green's function approach and the complex band-structure method in order to determine electronic and transport properties of those organic-semiconductor/metal (semiconductor) interfaces. We analyze one- and multi-bond nanocontact formation including structural modification (H desorption) as well as PPy length dependence. For selected ground state configurations of the considered interface systems we study their energetics and structural properties. Through the analysis of the local density of states, in particular isosurfaces of the charge density, the mechanism of the charge transfer and the charge neutrality levels are determined. The voltage dependence of the electrical conductance and the I-V characteristics are compared to the transport properties based on the complex band-structure method. The obtained results support recent experiments, where PPy nanowires are formed via electrochemical synthesis and placed between platinum or diamond microelectrodes.

Molecular scale energy dissipation in oligothiophene monolayers measured by dynamic force microscopy.

We perform a combined experimental and theoretical approach to establish the atomistic origin of energy dissipation occurring while imaging a molecular surface with an amplitude modulation atomic force microscope. We show that the energy transferred by a single nano-asperity to a sexithiophene monolayer is about 0.15 eV/cycle. The configuration space sampled by the tip depends on whether it approaches or withdraws from the surface. The asymmetry arises because of the presence of energy barriers among different deformations of the molecular geometry. This is the source of the material contrast provided by the phase-shift images.