  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 SC$_{18}H_{37}$ in a SC$_{18}H_{37}$ 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
100cm$^{-1}$, 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 $\approx$425cm$^{-1}$ down in energy to below $k_B
T$, 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.
