Abstract
Graphene adsorbed on Ru(0001) has been widely used as a template for adsorbing and isolating molecules, assembling organic-molecule structures with desired geometric and electronic properties and even inducing chemical reactions that are challenging to achieve in the gas phase. To fully exploit the potential of this substrate, for example, by being able to tune a graphene-based catalyst to perform optimally under specific conditions, it is crucial to understand the factors and mechanisms governing the molecule-substrate interaction. To contribute to this effort, we have conducted a combined experimental and theoretical study of the adsorption of cyanomethyl radicals (-CH(2)CN) on this substrate below room temperature by performing scanning tunneling microscopy experiments and density functional theory simulations. The main result is the observation that some -CH(2)CN molecules can jump back and forth between adsorption sites, while such dynamics is not seen above room temperature. We interpret this finding as the consequence of the molecules being adsorbed on a secondary adsorption configuration in which they are bound to the surface through the nitrogen atom. This secondary configuration is much less stable than the primary one, in which the molecule is bound through the -CH(2) carbon atom due to an sp(2)-to-sp(3) hybridization transition. The secondary configuration adsorption is achieved only when the cyanomethyl radical is deposited at low temperature. Increasing the substrate temperature provides the molecule with enough energy to reach the most stable adsorption configuration, thereby preventing the jumping.