Molecular Mechanics calculations for the adsorption of molecular switches on graphene

For the use of molecular switches in organic electronics, the adsorption properties of this class of molecules have to be understood on a variety of substrates. Spiropyran (SP) is a photochromic, three-dimensional molecular switch which can be converted to Merocyanine (MC), a planar isomer of Spiropyran where the central C-O bond has been broken. The adsorption behavior of various SP/MC species on graphene has been investigated using a combination of density functional theory and molecular mechanics calculations. The calculations show an adsorption geometry which favors nearly parallel configurations between aromatic rings in the adsorbate and substrate. Adsorption energies show direct dependence on the number of aromatic rings in the Merocyanine molecules. In a next step, identical molecules were adsorbed onto the substrate to mimic starting conditions for film growth with dimers as the initial step. Depending on the conformer geometries, parallel or anti-parallel orientations have been shown to be energetically more favorable depending on the location of inter-molecular ionic charge separation. Computationally predicting the onset of film growth and the respective unit cell geometry is an important step to identify large scale molecular films with microscopy and diffraction measurements.