Modeling the self-assembly of L-cysteine molecules on the Au(111) surface: A lattice model approach

• High-coverage l -cysteine SAMs on Au(111) were analyzed using SuSMoST toolkit • New stable adsorption patterns were identified and characterized by DFT • Intermolecular interactions dominate over surface site effects in stability • Bader charge analysis reveals differences in intra and intermolecular interactions • SuSMoST enables automated high-coverage SAM configuration generation The design of chiral materials with enhanced properties has rapidly gained interest. However, the complex modeling of self-assembled monolayers poses significant challenges to theoretical chemists, making it difficult to accurately predict or explain the structure and thermodynamic properties of adsorption layers in surface science. In the present work, we provide new insights into the self-assembly network of l -cysteine molecules on an Au(111) surface using a lattice model approach. The research focuses on the adsorption behavior of l -cysteine in its deprotonated acidic form [NH 3 + CH(CH 2 S - )COOH)], which introduces unique intermolecular interactions due to the charged amino group. Using the Surface Science Modeling and Simulation Toolkit (SuSMoST), we systematically explored multiple adsorption sites and configurations, generating unexplored high-coverage systems that were further analyzed at the density functional level of theory. Our findings highlight the significance of surface arrangements, intra- and inter-molecular interactions in determining the overall stability of the l -cysteine self-assembled monolayers. Among the various configurations analyzed, a newly identified system revealed the highest stability with an adsorption energy of -1.44 eV, competing with previously reported structures.