Stacked or Folded? Impact of Chelate Cooperativity on the Self-Assembly Pathway to Helical Nanotubes from Dinucleobase Monomers

Abstract

Self-assembled nanotubes exhibit impressive biological functions that have always inspired supramolecular scientists in their efforts to develop strategies to build such structures from small molecules through a bottom-up approach. One of these strategies employs molecules endowed with self-recognizing motifs at the edges, which can undergo either cyclization−stacking or folding−polymerization processes that lead to tubular architectures. Which of these self-assembly pathways is ultimately selected by these molecules is, however, often difficult to predict and even to evaluate experimentally. We show here a unique example of two structurally related molecules substituted with complementary nucleobases at the edges (i.e., G:C and A:U) for which the supramolecular pathway taken is determined by chelate cooperativity, that is, by their propensity to assemble in specific cyclic structures through Watson−Crick pairing. Because of chelate cooperativities that differ in several orders of magnitude, these molecules exhibit distinct supramolecular scenarios prior to their polymerization that generate self-assembled nanotubes with different internal monomer arrangements, either stacked or coiled, which lead at the same time to opposite helicities and chiroptical properties.

Non‐Innocent π Linkers Affect Cooperativity in Hydrogen‐Bonded Macrocycles

“…In other words, the hydrogen bonds between the Py‐Linker‐Ur monomers in the quartet are effectively more stabilizing than the hydrogen bonds in the dimer. The cooperative effect persists under experimental conditions as it still exists in the organic solvent (chloroform) utilized in experiments [9] (Table S9) and, as shown in previous work, [7a,9d,e] remains almost unaffected in layers of stacked systems. The cooperative effect in the quartets, however, becomes consistently less pronounced when the size of the acetylene linker increases, since the synergy reduces from −16.3 kcal mol −1 for PyUr to −7.2 kcal mol −1 for Py‐5‐Ur .…”

“…Recently, González‐Rodríguez and coworkers [9] obtained hydrogen‐bonded assembled quartets by the synthesis of a ditopic monomer which is based on guanosine and cytidine nucleosides at the termini, linked by a linear and rigid π‐conjugated p ‐diethynylbenzene linker. These quartets are prone to self‐assemble via a stacking mechanism, thereby forming tubular nanostructures [9e] …”

Supramolecular helix of an oligomeric azapeptide building block containing four β-turn structures

“…1 One strategy for constructing supramolecular helices is to elongate short building blocks in a helically folded conformation, through end-to-end noncovalent interactions. 1–4 Among them, aromatic foldamers of good predictability have been widely employed. 5–9 Those helices can be applied to the recognition, encapsulation and transport of a variety of ions and neutral molecules, 6,10–12 and the properties of the supramolecular helices can be altered by structural adjustments thus to achieve regulated selectivity and activity.…”