Free energy balance predicates dendrimer binding multivalency at molecular printboards

Self-assembled monolayers (SAMs) terminating in beta-cyclodextrin (beta-CD) 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 to the printboard, yielding more robust patterns. We performed fully atomistic molecular dynamics (MD) simulations in bulk explicit solvent to probe the conformational space available to dendrimer and dendrite ink molecules, in both free and bound environments. We show that accurate treatment of both pH effects and binding conformations gives calculated binding modes in line with known binding multivalencies. We identify and quantify the steric frustration causing small, low-generation dendrimer inks to bind to the printboard using just a subset of the available anchor groups. Furthermore, we show that the enhanced binding energy of multisite attachment offsets the steric strain, the feasibility of a given binding mode thus determined by the relative magnitudes of the unfavorable steric strain and favorable multisite binding free energies. We use our experimentally validated model of dendrimer binding to predict the binding mode of novel fluorophoric dendrites and find divalent binding, consistent with confocal microscopy imaging of pattern formation at molecular printboards.