Monolayer packing, dehydration, and ink-binding dynamics at the molecular

Gold-bound self-assembled monolayers (SAMs) terminating in β-cyclodextrin (β-CD) cavities provide a highly ordered surface array of hydrophobic binding pockets and so are used as "molecular printboards" for nanopatterning applications. The present work complements ongoing nanoscale experiments by providing the atom-scale structure, dynamics, and energetics of the printboard, which may aid the design of functional platforms for nanotechnology. We use fully atomistic molecular dynamics (MD) computer simulations to probe the printboard lattice constant, height, steric packing, hydrophobicity, and ink-binding properties as a function of gold-β-CD "linker" molecule and degree of binding to gold. The simulations reveal the stabilization associated with the experimentally observed surface lattice constant of ∼2 nm, alkanethioether linkers, and partial unbinding from gold. Additional ink-binding simulations indicate that multivalent ink molecules can offset disordering in the more loosely packed alkanethiol-linked printboard, with the attendant steric penalty similar in magnitude to the favorable multivalent ink:β-CD complexation.