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We have investigated the initial pentacene growth on the Si(111)--In surface using scanning tunneling microscopy. At a low coverage, the molecules lie down flat and form locally ordered molecular layers that are nucleated at the Si step edges. At a higher coverage, two kinds of pentacene crystals with the so-called herring-bone arrangement are grown directly on the surface with the longer molecular axis ('c' axis) being directed parallel to the surface. The pentacene growth on the surface is considered to be a 3D island growth mode. Two minor crystal structures that are poly-crystal and striped layer are also observed. All experimental results suggest that the surface is rather moderate compared with a reactive surface, which allows for molecular diffusion and rearrangement.

Realization of future hybrid electronic devices combining organic and inorganic semiconductors requires a well-defined interface between both components. Such an interface can be formed generally by self-ordering of organic molecules on inorganic substrates, which is usually hindered by strong covalent bonds to the semiconductor surface. In this paper, the 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) molecules were unexpectedly found to form a locally self-ordered monolayer on a strongly interacting semiconductor surface of the Ge(001). Molecular arrangements with preferential separations between the molecules were observed by the scanning tunneling microscopy at various coverages of the molecules and substrate temperatures, suggesting strong inter-molecular interaction. Atomic structures of two paired molecules and their inter-molecular interaction energies in five different configurations were calculated by density functional theory. Simple Monte Carlo simulations show that mobility of molecules activated only by the inter-molecular interactions is sufficient to reproduce the local self-ordering. A dominant inter-molecular interaction between neighboring chemisorbed molecules has mostly positive energy (destabilizing) except for a single configuration, which leads to the formation of one-dimensional chains of the molecules and finally a periodic two-dimensional array by increasing the coverage.

Adsorption structures of the 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) molecule on the clean Si(001) - 2 × 1 surface were investigated using scanning tunneling microscopy (STM) experiments in conjunction with first principles theoretical calculations. Four dominant adsorption structures were observed in the STM experiments and their atomic coordinates on the Si(001) surface were determined by comparison between the experimental STM images and the theoretical simulations. Maximizing the number of the Si-O bonds is more crucial than that of the Si-C bonds in the PTCDA adsorption.