The attachment of organic molecules to semiconductor surfaces and their measurement using scanning tunneling microscopy and spectroscopy (STM/STS) is considered to be a potential route toward conductance measurements of single molecules with known structural and electronic configuration. Here, we investigate a model systemacetophenone on Si(001)and demonstrate that this adsorbate can be manipulated using the STM such that it adopts a configuration where it stands upright with a free-standing phenyl ring and strong Si–O linkage to the substrate. For the structural identification we combine STM imaging with density functional theory (DFT) calculations to describe the adsorbate structures that were observed in our experiments and the reaction pathways that link them; of these the upright configuration is the most thermodynamically stable. The chemical structure of the upright configuration suggests that π-conjugation within the adsorbate extends to the silicon surface resulting in strong hybridization of the molecular states with the substrate. This is supported by the absence of any significant features in STS curves recorded over the adsorbate. The structure of this adsorbate and its robust attachment to silicon makes it attractive for future STM/semiconductor-based molecular conductance measurements.

Using density functional theory, we report detailed reaction path calculations for the reaction of acetone with the silicon (001) surface. We identify the key reaction intermediates of dissociative adsorption and the transition states between them. This resolves the identity of the one-dimer intermediate observed in STM experiments and its role in the formation of several two-dimer-wide end products of dissociation. Key to the understanding of the dissociation mechanism is the ambiphilic character of the two reactants, that is the simultaneous expression of electrophilic and nucleophilic reactivities in both the surface and the acetone molecule.

Assembling molecular components into low-dimensional structures offers new opportunities for nanoscale device applications. Here we describe the self-assembly of indium atoms into metallic chains on the silicon (001) surface using adsorbed benzonitrile molecules as nucleation and termination sites. Critically, individual benzonitrile adsorbates can be manipulated using scanning tunneling microscopy. This affords control over the position and orientation of the molecular adsorbates, which in turn determine the origin, direction, and length of the self-assembled metallic chains.

A detailed understanding of the chemical reactions of organic molecules with semiconductor surfaces will greatly aid schemes for the incorporation of organic functionality into existing technologies. In this paper we report on the reaction of acetaldehyde (CH3CHO) with silicon (001) as revealed by a combination of temperature-dependent scanning tunneling microscopy (STM) experiments and density functional theory (DFT). We observe that low-coverage exposures at room temperature result almost exclusively in the formation of a single adsorbate species. Conversion of this structure into thermodynamically favored bridge-bonded structures is achieved through temperature anneals between 150–250 °C. We determine the chemical identity of each of the experimentally observed species by comparison with DFT total energy calculations and simulated STM images. Calculations of transition states are used to formulate a full reaction pathway explaining the formation of the observed species. Excellent agreement is found between our experimental measurements and theoretical calculations. The results also present a picture consistent with our previous work on acetone and reveal a general reaction pattern for molecules containing the acetyl COCH3 functional group, where the initial attachment to the surface is mediated by a carbonyl C=O group. This suggests that modification of the residue R will facilitate in binding other electronically active molecules to the surface in a controlled fashion.

It has been observed in scanning tunneling microscopy (STM) that the adsorption of molecules on the (001) surface of a Group IV semiconductor can lead to an asymmetric ordering of the dimers immediately adjacent to the adsorbate. This so-called pinning may occur along the dimer row on only one, or both sides of the adsorbate. Here we present a straightforward methodology for predicting such pinning and illustrate this approach for several different adsorbate structures on the Si(001) surface. This approach extends earlier work by including the effects of coupling across the adsorbate as well as the nearest-neighbor interactions between the chemisorbed dimer and its adjacent dimers. The results are shown to be in excellent agreement with the room temperature experimental STM data. The examples also show how this approach can serve as a powerful tool for discriminating between alternative possible adsorbate structures on a dimerized semiconductor (001) surface, especially in cases of molecular adsorption where the STM measurements provide insufficient details of the underlying atomic structure.