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Abstract This work investigates the influence of dielectrophoretic forces on the structural features and the resulting aggregates of a chromogenic model system, peptide‐diacetylene (D₃GV‐DA) amphiphiles. Here, we systematically investigate how non‐uniform electric fields impact the (i) peptide‐directed supramolecular assembly stage and (ii) topochemical photopolymerization stage of polydiacetylenes (PDAs) in a quadrupole‐based dielectrophoresis (DEP) device, as well as the (iii) manipulation of D₃GV‐DA aggregates in a light‐induced DEP (LiDEP) platform. The conformation‐dependent chromatic phases of peptide‐PDAs are utilized to probe the chain‐level effect of DEP exposure after the supramolecular assembly or after the topochemical photopolymerization stage. Steady‐state spectroscopic and microscopy analyses show that structural features such as the chirality and morphologies of peptidic 1‐D nanostructures are mostly conserved upon DEP exposure, but applying mild, non‐uniform fields at the self‐assembly stage is sufficient for fine‐tuning the chromatic phase ratio in peptide‐PDAs and manipulating their aggregates via LiDEP. Overall, this work provides insights into how non‐uniform electric fields offer a controllable approach to fine‐tune or preserve the molecularly preset assembly order of DEP‐responsive supramolecular or biopolymeric assemblies, as well as manipulate their aggregates using light projections, which have future implications for the precision fabrication of macromolecular systems with hierarchical structure‐dependent function.