Quantum Mechanical Derived (VdW-DFT) Transferable Lennard–Jones and Morse Potentials to Model Cysteine and Alkanethiol Adsorption on Au(111)

Abstract

The cysteine and alkanethiol adsorption on Au(111) surfaces is investigated using density functional theory (DFT) and classic molecular dynamics (MD). Understanding the S–Au interaction across different scales poses major challenges. DFT provides atomic-level precision but it hardly provides insight on nanosecond scale dynamics of this interface. Alternatively, MD, although it enables modeling larger systems for longer periods, its accuracy heavily relies on the parameterization of the force fields (FF). To address this, an MD potential is fitted using DFT calculations, bridging the gap in accuracy and efficiency. At the DFT level, it is found that PBE with DFT-D3 reproduces complex approaches at a fraction of the computational cost. Separating PBE and DFT-D3 contributions reveals consistent PBE energy across molecules (chemisorption), while dispersion varies (physisorption). Thus, the interaction energy of cysteine and two short-chain alkanethiols is calculated to parameterize both Morse and Lennard–Jones (LJ) potentials. The parameterization improves the potential energy in the preferred adsorption sites: the threefold hcp and fcc with respect to the previous proposals in the literature. Furthermore, the transferability is here demonstrated. At last, these results show that LJ potentials outperform more complex Morse potentials. The procedure is general, and the codes and supporting inputs are publicly available, allowing swift generation of potential energy surfaces (PES) at the DFT level, and fitted LJ or Morse potentials to any molecular interface.