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.

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.

The phonon dynamics of the Sn/Ge(111) interface is studied using high-resolution helium atom scattering and first-principles calculations. At room temperature we observe a phonon softening at the Kmacr; point in the (sqrt[3]xsqrt[3])R30 degrees phase, associated with the stabilization of a (3x3) phase at low temperature. That phonon band is split into three branches in the (3x3) phase. We analyze the character of these phonons and find out that the low- and room-temperature modes are connected via a chaotic motion of the Sn atoms. The system is shown to present an order-disorder transition.