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

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.

Self-Sorting Governed by Chelate Cooperativity.

Self-sorting phenomena are the basis of manifold relevant (bio)chemical processes where a set of molecules is able to interact with no interference from other sets and are ruled by a number of codes that are programmed in molecular structures. In this work, we study, the relevance of chelate cooperativity as a code for achieving high self-sorting fidelities. In particular, we establish qualitative and quantitative relationships between the cooperativity of a cyclic system and the self-sorting fidelity when combined with other molecules that share identical geometry and/or binding interactions. We demonstrate that only systems displaying sufficiently strong chelate cooperativity can achieve quantitative narcissistic self-sorting fidelities either by dictating the distribution of cyclic species in complex mixtures or by ruling the competition between the intra- and intermolecular versions of a noncovalent interaction.

Dual-Mode Chiral Self-Assembly of Cone-Shaped Subphthalocyanine Aromatics.

Columnar polymers and liquid crystals obtained from π-conjugated cone-shaped molecules are receiving increasing interest due to the possibility of obtaining unconventional polar organizations that show anisotropic charge transport and unique chiroptical properties. However, and in contrast to the more common planar discotics, the self-assembly of conic or pyramidic molecules in solution remains largely unexplored. Here, we show how a molecular geometry change, from flat to conic, can generate supramolecular landscapes where different self-assembled species, each of them being under thermodynamic equilibrium with the monomer, exist exclusively within distinct regimes. In particular, depending on the solvent nature-aromatic or aliphatic-cone-shaped C3-symmetric subphthalocyanine 1 can undergo self-assembly either as a tail-to-tail dimer, showing monomer-dimer sigmoidal transitions, or as a head-to-tail noncentrosymmetric columnar polymer, exhibiting a nucleation-elongation polymerization mechanism. Moreover, the experimental and theoretical comparison between racemic and enantiopure samples revealed that the two enantiomers (1M and 1P) tend to narcissistically self-sort in the dimer regime, each enantiomer showing a strong preference to associate with itself, but socially self-sort in the polymer regime, favoring an alternate stacking order along the columns.

Noncovalent Synthesis of Self-Assembled Nanotubes through Decoupled Hierarchical Cooperative Processes.

Because of their wide number of biological functions and potential applications, self-assembled nanotubes constitute highly relevant targets in noncovalent synthesis. Herein, we introduce a novel approach to produce supramolecular nanotubes with defined inner and outer diameters from rigid rod-like monomers programmed with complementary nucleobases through two distinct, decoupled cooperative processes of different hierarchy and acting in orthogonal directions: chelate cooperativity, responsible for the formation of robust Watson-Crick H-bonded cyclic tetramers, and nucleation-growth cooperative polymerization.

Impact of Conformational Effects on the Ring-Chain Equilibrium of Hydrogen-Bonded Dinucleosides.

Supramolecular ring-versus-chain equilibria are ubiquitous in biological and synthetic systems. Understanding the factors that decide whether a system will fall on one side or the other is crucial to the control of molecular self-assembly. This work reports results with two kinds of dinucleoside monomers, in which the balance between closed cycles and open polymers is found to depend on subtle factors that rule conformational equilibria, such as steric hindrance, intramolecular interactions, or π-conjugation pathways.

How Large Can We Build a Cyclic Assembly? Impact of Ring Size on Chelate Cooperativity in Noncovalent Macrocyclizations.

Self-assembled systems rely on intramolecular cooperative effects to control their growth and regulate their shape, thus yielding discrete, well-defined structures. However, as the size of the system increases, cooperative effects tend to dissipate. We analyze here this situation by studying a set of oligomers of different lengths capped with guanosine and cytidine nucleosides, which associate in cyclic tetramers by complementary Watson-Crick H-bonding interactions. As the monomer length increases, and thus the number of C(sp)-C(sp2 ) σ-bonds in the π-conjugated skeleton, the macrocycle stability decreases due to a notable reduction in effective molarity (EM), which has a clear entropic origin. We determined the relationship between EM or ΔS and the number of σ-bonds, which allowed us to predict the maximum monomer lengths at which cyclic species would still assemble quantitatively, or whether the cyclic species would not able to compete at all with linear oligomers over the whole concentration range.

Role of the Symmetry of Multipoint Hydrogen Bonding on Chelate Cooperativity in Supramolecular Macrocyclization Processes.

Herein, we analyze the intrinsic chelate effect that multipoint H-bonding patterns exert on the overall energy of dinucleoside cyclic systems. Our results indicate that the chelate effect is regulated by the symmetry of the H-bonding pattern, and that the effective molarity is reduced by about three orders of magnitude when going from the unsymmetric ADD-DAA or DDA-AAD patterns to the symmetric DAD-ADA pattern.

High-fidelity noncovalent synthesis of hydrogen-bonded macrocyclic assemblies.

A hydrogen-bonded cyclic tetramer is assembled with remarkably high effective molarities from a properly designed dinucleoside monomer. This self-assembled species exhibits an impressive thermodynamic and kinetic stability and is formed with high fidelities within a broad concentration range.

Non-centrosymmetric homochiral supramolecular polymers of tetrahedral subphthalocyanine molecules.

A combination of spectroscopy (UV/Vis absorption, emission, and circular dichroism), microscopy (AFM and TEM), and computational studies reveal the formation of non-centrosymmetric homochiral columnar subphthalocyanine assemblies. These assemblies form through a cooperative supramolecular polymerization process driven by hydrogen-bonding between amide groups, π-π stacking, and dipolar interactions between axial B-F bonds.

The Role of Peripheral Amide Groups as Hydrogen-Bonding Directors in the Tubular Self-Assembly of Dinucleobase Monomers.

Nanotubes are a fascinating kind of self-assembled structure which have a wide interest and potential in supramolecular chemistry. We demonstrated that nanotubes of defined dimensions can be produced from dinucleobase monomers through two decoupled hierarchical cooperative processes: cyclotetramerization and supramolecular polymerization. Here we analyze the role of peripheral amide groups, which can form an array of hydrogen bonds along the tube axis, on this self-assembly process. A combination of 1 H NMR and CD spectroscopy techniques allowed us to analyze quantitatively the thermodynamics of each of these two processes separately. We found out that the presence of these amide directors is essential to guide the polymerization event and that their nature and number have a strong influence, not only on the stabilization of the stacks of macrocycles, but also on the supramolecular polymerization mechanism.

Understanding complex supramolecular landscapes: non-covalent macrocyclization equilibria examined by fluorescence resonance energy transfer.

As molecular self-assembled systems increase in complexity, due to a large number of participating entities and/or the establishment of multiple competing equilibria, their full understanding becomes likewise more complicated, and the use of diverse analytical techniques that can afford complementary information is required. We demonstrate in this work that resonance excitation energy transfer phenomena, measured by fluorescence spectroscopy in combination with other optical spectroscopies, can be a valuable tool to obtain supplementary thermodynamic data about complex supramolecular landscapes that other methods fail to provide. In particular, noncovalent macrocyclization processes of lipophilic dinucleosides are studied here by setting up a competition between intra- and intermolecular association processes of Watson-Crick H-bonding pairs. Multiwavelength analysis of the monomer emission changes allowed us to determine cyclotetramerization constants and to quantify chelate cooperativity, which was confirmed to be substantially larger for the G-C than for the A-U pair. Furthermore, when bithiophene-BODIPY donor-acceptor energy transfer probes are employed in these competition experiments, fluorescence and circular dichroism spectroscopy measurements in different regions of the visible spectrum additionally reveal intermolecular interactions occurring simultaneously at both sides of the macrocyclization reaction: the cyclic product, acting as a host for the competitor, and the monomer reactant, ultimately leading to macrocycle denaturation.

Reversible dispersion and release of carbon nanotubes via cooperative clamping interactions with hydrogen-bonded nanorings.

Due to their outstanding electronic and mechanical properties, single-walled carbon nanotubes (SWCNTs) are promising nanomaterials for the future generation of optoelectronic devices and composites. However, their scarce solubility limits their application in many technologies that demand solution-processing of high-purity SWCNT samples. Although some non-covalent functionalization approaches have demonstrated their utility in extracting SWCNTs into different media, many of them produce short-lived dispersions or ultimately suffer from contamination by the dispersing agent. Here, we introduce an unprecedented strategy that relies on a cooperative clamping process. When mixing (6,5)SWCNTs with a dinucleoside monomer that is able to self-assemble in nanorings via Watson-Crick base-pairing, a synergistic relationship is established. On one hand, the H-bonded rings are able to associate intimately with SWCNTs by embracing the tube sidewalls, which allows for an efficient SWCNT debundling and for the production of long-lasting SWCNT dispersions of high optical quality along a broad concentration range. On the other, nanoring stability is enhanced in the presence of SWCNTs, which are suitable guests for the ring cavity and contribute to the establishment of multiple cooperative noncovalent interactions. The inhibition of these reversible interactions, by just adding, for instance, a competing solvent for hydrogen-bonding, proved to be a simple and effective method to recover the pristine nanomaterial with no trace of the dispersing agent.

Hydrogen-Bonded Macrocyclic Supramolecular Systems in Solution and on Surfaces.

Cyclization into closed assemblies is the most recurrent approach to realize the noncovalent synthesis of discrete, well-defined nanostructures. This review article particularly focuses on the noncovalent synthesis of monocyclic hydrogen-bonded systems that are self-assembled from a single molecule with two binding-sites. Taking advantage of intramolecular binding events, which are favored with respect to intermolecular binding in solution, can afford quantitative amounts of a given supramolecular species under thermodynamic control. The size of the assembly depends on geometric issues such as the monomer structure and the directionality of the binding interaction, whereas the fidelity achieved relies largely on structural preorganization, low degrees of conformational flexibility, and templating effects. Here, we discuss several examples described in the literature in which cycles of different sizes, from dimers to hexamers, are studied by diverse solution or surface characterization techniques.