Bumm, LloydBhattacharya, Soumya2021-12-202021-12-202021-12https://hdl.handle.net/11244/332399Self-assembled monolayers (SAMs) of alkanethiol molecules have been widely studied over the last three decades because of their diverse applications in the biomedical, nanotechnology, surface science, and electronics. It is also regarded as the model system to study the binding of organic molecules on the metal surfaces via thiol functional group. The robustness of the SAM structure combined with the ease of preparation makes it an ideal candidate for both fundamental and applied research. The structure of the alkanethiol SAMs on the Au(111) substrate is determined by the interplay between the alkyl chain packing and the interaction at the Au-S interface. Although our understanding of the SAM structure has significantly advanced over the last 35 years, an unambiguous atomic description of the Au-S interface and its influence on the chain packing remains elusive. In order to have better control of the SAM structure for different applications, we require a better understanding of the alkanethiol monolayer. In this work, we use a reductionist approach to determine the preferred head group positions driven by the chain packing, and by the interaction at the Au-S interface, separately. We use molecular dynamics (MD) to study the chain packing of the dense phase saturation coverage decanethiol SAM, and density functional theory (DFT) to study the interaction at the Au-S interface using an isolated methanethiol adsorbate. Alkane chains prefer a close-packed structure for the efficient interlocking of the methylene groups that minimizes the energy of the system. The molecular plane adjusts its orientation (molecular twist) depending on the spacing and the symmetry of the head groups to achieve a close packing of the chains. We first constrain the head groups at the high symmetry (√3 × √3)R30° sites to study the preferred combination of the molecular twists. We use this result as our baseline to study the effect of chain packing on the head group offset from the (√3 × √3)R30° sites. The position of the head groups also depends on the interaction at the Au-S interface. The preferred sites are determined by the tetrahedral coordination and the sp3 hybridization of the sulfur head groups. Relaxation and reconstruction (involve adatoms and/or surface vacancies) of the substrate also has significant influence on the preferred adsorption sites. We begin by determining the preferred positions of the head group on the unrelaxed substrate driven by the interaction at the Au-S interface alone. We then use the unrelaxed substrate as our reference to study the effect of substrate relaxation on the head group positions. To simulate a realistic model of the technologically interesting long-chain dense-phase alkanethiol SAM, we need to combine the effect of the chain packing and the interaction at the Au-S interface. Currently, we do not have a site-dependent force field for the Au-S interface to simulate the SAM structure using MD. On the other hand, the size of the problem is computationally too large for the DFT method. We demonstrated an approach to bridge the computational gap by using the atomic structure at the Au-S interface predicted by the DFT to study the effect on the chain packing. Using our DFT results, we predicted the symmetry of the adsorption site dependent dihedral force fields that can be used in MD to improve the prediction of the SAM structure.self-assembled monolayerdensity functional theoryalkanethiolmolecular dynamicsAu substrate