A refined atomistic model of functionalized self-assembled monolayers on gold: Assessment of force field parameters

Self-assembled monolayers (SAMs) of alkanethiols on gold surfaces are important for various technological applications, such as electroanalytical sensors, organic electronic devices, and catalysts. However, providing a consistent computational description of the unique structural features of these SAMs, such as adsorption patterns, chain conformations, and superlattice arrangements, is challenging, particularly within a versatile computational framework that can simulate both the structural features of these systems and their irradiation-driven chemical transformations. This study systematically analyzes molecular mechanics force field parameters for bonded and nonbonded (van der Waals and electrostatic) interactions in alkanethiol SAMs with different terminal groups. Using structure optimization and energy decomposition analysis, we assess the impact of force field parameters on key properties, such as the equilibrium tilt angle, ligand packing density, and nanoscale structural organization. Based on this detailed benchmarking, an optimal set of force field parameters has been identified that reproduces the experimentally determined structural and energetic properties of SAMs and ensures their dynamic stability at room temperature. This provides a validated framework for simulating pristine and functionalized alkanethiol-coated substrates under thermal conditions relevant to experimental applications.