Assessment of Molecular Dynamics simulations for self-assembly based electronics

As the interest in molecular-scale devices grows, so does the importance of simulation methods capable of investigating the properties of systems of that size. One method is molecular dynamics (MD). It solves a discretization of Newton’s equation of motion on a system of atoms, treated as point particles, provided the initial configuration, the boundary conditions, and a model of the potentials acting on the atoms. This work focuses on the application of molecular dynamics to study the formation of molecular self-assembled monolayers (SAMs). The purpose is to see whether such technology can contribute to the study of systems of interest in the field of molecular electronics. The study, in particular, provides insights on the behavior of the 6(ferrocenyl)hexanethiol molecule, a molecule composed by a hexane chain terminated with a thiol group on one side and a ferrocene group on the other side. Such a molecule has potential application in the development of molecular diodes and, more in general, thiolated ferrocenyl molecules are promising for the implementation of Beyond-CMOS technologies. There has been, however, little exploration so far of its behavior in molecular dynamics simulation. This work is structured in three parts. The first part shows an attempt to deposit simple 1-hexanethiol molecules on a gold substrate using first a reactive force field, reaxFF, then a united atom force field, where the hydrogen atoms are left implicit. The former is too computationally intensive. Also, a SAM does not form. The latter instead succeeds in assembling in an orderly pattern. The second part concerns the study of the formation and the properties of self-assembled monolayers of 6(ferrocenyl-hexanethiol) molecules on a gold substrate. The analysis focuses on two different types of simulation: a simulated deposition where the molecules are left free to spread on the substrate and a simulation of final configurations where the molecules are anchored in a regular superlattice. This work compares the quantitative analysis of the geometry of both types of systems with the available experimental data on real systems. The scarcity of such experimental data means that they can help gauge the validity of the molecular dynamics simulation but without providing conclusive evidence in that respect. This work shows how the choice of potential strongly impacts the simulation result. A complete and accurate model of all the parameters, especially of the bond between gold and sulfur, is challenging to obtain. Thus, there is a certain degree of mismatch between some results obtained in this work and the experiments, mostly regarding the tilt of the alkyl chain. However, there is a clear path to improve as long as the data available increases to guide future work. The third part shows the deposition of the 6(ferrocenyl)hexanethiol molecules on wires of different sizes. This allows to study its distribution on the wire and its behavior when oxidized and subjected to an external electric field in the z-direction. Here the molecules pack very densely. Furthermore, the intermolecular repulsion caused by the oxidized charge prevents some molecules from lifting from a horizontal position even when subjected to a 2 V/nm electric field. This study provides some insight into the formation of molecular wires and the first-order response to an electric field. However, experimental data is needed to validate the results and the parameters used.