In general, the nature of the chemical linker group connecting the molecules to electrodes is a critically determinant factor influencing the transport properties through single molecular junctions [1], because they organize the energy gap alignment between the highest occupied molecular orbitals (HOMO)/lowest unoccupied molecular orbitals (LUMO) of molecule and electrode Fermi level. Therefore, comprehensive studies on the molecule-metal contact and appropriate choice of linkers would be essential for the development of molecular circuits. Ferrocene, belonging to the metallocene complexes with the formula FeC5H10, has been widely suggested in molecular electronic devices due to its exclusive features such as high degree of chemical and thermal stability and high structural flexibility [2,3]. Ferrocene-based nanoscale devices have been the subject of many theoretical and experimental investigations [4-6]. In this study, we demonstrate that how the nano-contacts affect the the electron transfer process of the metall-organic molecules, such as ferrocene. Our model system which is shown in Fig. 1, consists of a single ferrocene molecule attached to gold electrodes via linkers as Au(100)-S-Fe(Cp)2-X-Au(100) conformation, where X is S and NH2 linker. All calculations are performed based on density functional theory (DFT) plus a non-equilibrium Green’s function (NEGF) method. The generalized gradient approximation (GGA) is used for calculating the exchange correlation function. Geometry Optimization and electronic structure calculations have been performed in SIESTA package [7] and transport calculations are implemented in TRANSIESTA code [8].
