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When strands of DNA encapsulate silver clusters, supramolecular optical chromophores develop. However, how a particular structure endows a specific spectrum remains poorly understood. Here, we used neutron diffraction to map protonation in (A<sub>2</sub>C<sub>4</sub>)<sub>2</sub>-Ag<sub>8</sub>, a green-emitting fluorophore with a "Big Dipper" arrangement of silvers. The DNA host has two substructures with distinct protonation patterns. Three cytosines from each strand collectively chelate handle-like array of three silvers, and calorimetry studies suggest Ag<sup>+</sup> cross-links. The twisted cytosines are further joined by hydrogen bonds from fully protonated amines. The adenines and their neighboring cytosine from each strand anchor a dipper-like group of five silvers via their deprotonated endo- and exocyclic nitrogens. Typically, exocyclic amines are strongly basic, so their acidification and deprotonation in (A<sub>2</sub>C<sub>4</sub>)<sub>2</sub>-Ag<sub>8</sub> suggest that silvers perturb the electron distribution in the aromatic nucleobases. The different protonation states in (A<sub>2</sub>C<sub>4</sub>)<sub>2</sub>-Ag<sub>8</sub> suggest that atomic level structures can pinpoint how to control and tune the electronic spectra of these nanoscale chromophores.
Published in: Dialnet (Universidad de la Rioja)
Volume 13, Issue 48, pp. 11317-11322