title: The effective concentration of unbound ink anchors at the molecular printboard.
abstract: Self-assembled monolayers terminating in beta-cyclodextrin cavities can be used to bind ink molecules and so provide a molecular printboard for nanopatterning applications. Multivalent or multisite binding strengthens the attachment of large inks and provides more robust patterns. In the present work we use computer simulations to probe the behavior of functionalized dendrimer inks at the printboard. We performed a series of long 10 ns fully atomistic molecular dynamics (MD) simulations to measure the effective local concentration of unbound ink anchor groups at the printboard for a variety of binding modes and also for the partial unbinding prerequisite for ink diffusion on the printboard. These simulations allow us to describe the conformational space occupied by partially bound inks and estimate the likelihood of an additional binding interaction. Furthermore, by simulating the shift from a divalent to monovalent binding mode we show that the released anchor quickly moves to the periphery of the dendrimer binding hemisphere but then reapproaches the printboard and remains in the vicinity of alternative binding sites. Secondary electrostatic interactions between the protonated dendrimer core and hydroxyl groups at the entrance to the beta-cyclodextrin cavities give "flattened" dendrimer binding orientations and may aid dendrimer diffusion on the printboard, allowing the dendrimer to "walk" along the printboard by switching between different partially bound states and minimizing complete unbinding to bulk solution, crucial for the application of the printboard in, for example, medical diagnostics.
authors.affiliation: Tyndall National Institute, Prospect Row, Lee Maltings, Cork, Ireland. damien.thompson@tyndall.ie
authors.forename: D
authors.initials: D
authors.lastname: Thompson