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

Ella Matthews

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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 kBT, 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.
Original languageEnglish
Number of pages26
JournalPhysical Chemistry Chemical Physics
Publication statusAcceptance date - 2015


  • computational chemistry
  • Theoretical simulation
  • self-assembled monolayers
  • chemistry
  • normal mode analysis
  • thin-films
  • Molecular mechanics


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