Self-assembled monolayer molecule dynamics are perturbed by surface- and surrounding monolayer-derived geometrical confinement

The surface a thin-film is attached to and the surrounding monolayer causes geometrical confinement of a interrogated molecule; we look at the base case of a SC₁₈H₃₇ in a SC₁₈H₃₇ monolayer on Au[111]. Normal mode analysis was used to get vibrations, and these are analysed using mode character indicators which can quantify: how active an element is in a mode; the overall direction of the mode; and which chemical coordinates are relevant. We examined the 4 possible packing structures. We find that the more thermodynamically stable structures were less perturbed by the surface and more supported by the surrounding monolayer. The surface-perturbed modes were below 100^-1, had a higher global, carbon, sulfur, longitudinal and torsional characters, indicating unit cell backbone motions, often with increased S motion parallel to the surface, and an increased terminal methyl group motion. Modes identified by this technique showed a difference between experimental vibrations (with and without the surface) that was twice as large as those not identified. The surrounding monolayer had a larger effect on a single molecule dynamics than the surface, including stabilising the molecules enough for 12 high energy modes to move ≈$425^-1 down in energy to below ^k_BT, allowing them to be populated at room temperature. These modes had higher local and higher H characters, and were highly modulated by the SAM structure. This work shows novels ways to analyse vibrations, and demonstrates the crucial need to include geometric confinement effects in SAM studies.