Toward the development of a practical molecular computing scheme, certain molecules are thought to be able to perform quantum state switching at room temperature (for example, digital bit 1 to 0). For the implementation of logic functions, these molecules must be arranged on surfaces in a controlled manner. The Creutz-Taube molecule [(NH3)(5)Ru(pyrazine)Ru(NH3)(5)] X (o-toluenesulphonate)(5) (CT5) can be viewed as a two-dot molecule for the purposes of molecular computing. We report here nanopatterning of CT5 molecules through the use,of electron-beam lithography (EBL) and poly(methylmethacrylate) (PMMA) electron resist. After development of electron-beam modified PMMA films on SiO2, trenches with exposed surfaces were formed. These wafers were then soaked in CT5 aqueous solution. Atomic force microscopy and x-ray photoelectron spectroscopy were used to investigate the surface characteristics of wafers after dissolution of the PMMA and to confirm the binding of a monolayer of CT5 molecules on the wafer within the areas delimited by the PMMA trenches. CT5 molecules were deposited as a monolayer. with two Ru atoms lying on the SiO2 surface. 35-nm-wide lines of a monolayer of CT5 molecules on a SiO2 surface were demonstrated. (C) 2003 American Vacuum Society.