Scanning tunneling microscopy simulations of poly(3-dodecylthiophene) chains adsorbed on highly oriented pyrolytic graphite

We report on a novel scheme to perform efficient simulations of Scanning Tunneling Microscopy (STM) of molecules weakly bonded to surfaces. Calculations are based on a tight binding (TB) technique including self-consistency for the molecule to predict STM imaging and spectroscopy. To palliate the lack of self-consistency in the tunneling current calculation, we performed first principles density-functional calculations to extract the geometrical and electronic properties of the system. In this way, we can include, in the TB scheme, the effects of structural relaxation upon adsorption on the electronic structure of the molecule. This approach is applied to the study of regioregular poly(3-dodecylthiophene) (P3DDT) polymer chains adsorbed on highly oriented pyrolytic graphite (HOPG). Results of spectroscopic calculations are discussed and compared with recently obtained experimental datComment: 15 pages plus 5 figures in a tar fil

QM/MM methods for crystalline defects. Part 1: Locality of the tight binding model

The tight binding model is a minimal electronic structure model for molecular modelling and simulation. We show that the total energy in this model can be decomposed into site energies, that is, into contributions from each atomic site whose influence on their environment decays exponentially. This result lays the foundation for a rigorous analysis of QM/MM coupling schemes.Comment: 35 pages, 3 figure

A first-principles approach to electrical transport in atomic-scale nanostructures

We present a first-principles numerical implementation of Landauer formalism for electrical transport in nanostructures characterized down to the atomic level. The novelty and interest of our method lies essentially on two facts. First of all, it makes use of the versatile Gaussian98 code, which is widely used within the quantum chemistry community. Secondly, it incorporates the semi-infinite electrodes in a very generic and efficient way by means of Bethe lattices. We name this method the Gaussian Embedded Cluster Method (GECM). In order to make contact with other proposed implementations, we illustrate our technique by calculating the conductance in some well-studied systems such as metallic (Al and Au) nanocontacts and C-atom chains connected to metallic (Al and Au) electrodes. In the case of Al nanocontacts the conductance turns out to be quite dependent on the detailed atomic arrangement. On the contrary, the conductance in Au nanocontacts presents quite universal features. In the case of C chains, where the self-consistency guarantees the local charge transfer and the correct alignment of the molecular and electrode levels, we find that the conductance oscillates with the number of atoms in the chain regardless of the type of electrode. However, for short chains and Al electrodes the even-odd periodicity is reversed at equilibrium bond distances.Comment: 14 pages, two-column format, submitted to PR

The role of contacts in molecular electronics

Molecular electronic devices are the upmost destiny of the miniaturization trend of electronic components. Although not yet reproducible on large scale, molecular devices are since recently subject of intense studies both experimentally and theoretically, which agree in pointing out the extreme sensitivity of such devices on the nature and quality of the contacts. This chapter intends to provide a general theoretical framework for modelling electronic transport at the molecular scale by describing the implementation of a hybrid method based on Green function theory and density functional algorithms. In order to show the presence of contact-dependent features in the molecular conductance, we discuss three archetypal molecular devices, which are intended to focus on the importance of the different sub-parts of a molecular two-terminal setup.Comment: 17 pages, 8 figure