We present results of molecular dynamics simulations of the interaction of a 48 amino acid peptide, carnobacteriocin B2, with model hydrophobic, anionic, and cationic self-assembled monolayers (SAMs). The model monolayers were formed by placing alkanethiols, HS-(CH2)(10)-X, where the terminal functional group X was chosen to be CH3, COO-, or NH3+. The carboxylate and amine groups were modeled as either fully charged or partially charged. Furthermore, simulations are presented for nanopatterned SAMs consisting of parallel stripes of hydrophobic/anionic and anionic/cationic SAMs. These simulations help elucidate the mechanisms of interaction of the peptide with model surfaces that emulate the chemical heterogeneity of lipid bilayer membranes or peptide nanoarrays. The simulation results depict how the nanoscale chemical heterogeneity of surfaces can simultaneously alter the peptides interaction with the surface and its secondary structure. Hydrophobic interactions result in the strongest adsorption of the peptide to the monolayer, simultaneously maintaining the structural integrity of the peptide. Electrostatic interactions, on the other hand, tend to enhance the solvation of the peptide, thereby causing radical changes in the secondary structure.