Multiscale modelling of organic molecules interacting with solids

This Ph.D. thesis concerns the application of computational chemistry methods to molecular systems of interest, in collaboration with experimental research groups. The bulk of the work was focused on self-assembled monolayers (SAM) of thiol molecules on gold surfaces. SAMs are of central interest in surface science; they are studied for potential applications, among others, in nanolithography, biosensing, and electronics. The nature of the sulfur/gold interface is still debated: although it is commonly held that the –SH moiety dissociates to form a covalent S-Au bond, several studies report SAMs of undissociated thiols. To get insights on this point, we combined density functional theory (DFT) and molecular dynamics (MD) simulations to study in detail the thermodynamics of SAM formation on gold surfaces, using 7-mercapto-4-methylcoumarin (MMC) and 3-mercaptopropionic acid (MPA) as model molecules. The chemical potential of a thiol molecule in the SAM was computed by MD thermodynamic integration as a function of the SAM density; the maximum SAM densities for MMC and MPA in dissociated and undissociated form were computed and compared with experimental results.