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

  • Marina González-Sánchez
    Marina González-Sánchez
    Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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    Orcidhttps://orcid.org/0000-0002-2292-0794
  • , 
  • María J. Mayoral
    María J. Mayoral
    Department of Inorganic Chemistry, Universidad Complutense de Madrid, 28040 Madrid, Spain
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    Orcidhttps://orcid.org/0000-0001-7156-5939
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  • Violeta Vázquez-González
    Violeta Vázquez-González
    Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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  • , 
  • Markéta Paloncýová
    Markéta Paloncýová
    Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
    Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 779 00 Olomouc, Czech Republic
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    Orcidhttps://orcid.org/0000-0002-6811-7761
  • , 
  • Irene Sancho-Casado
    Irene Sancho-Casado
    Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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    Orcidhttps://orcid.org/0000-0002-3119-4157
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  • Fátima Aparicio
    Fátima Aparicio
    Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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  • Alberto de Juan
    Alberto de Juan
    Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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  • Giovanna Longhi
    Giovanna Longhi
    Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
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    Orcidhttps://orcid.org/0000-0002-0011-5946
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  • Patrick Norman
    Patrick Norman
    Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
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    Orcidhttps://orcid.org/0000-0002-1191-4954
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  • Mathieu Linares*
    Mathieu Linares
    Laboratory of Organic Electronics and Scientific Visualization Group, ITN, Campus Norrköping; Swedish e-Science Research Centre (SeRC), Linköping University, 58183 Linköping, Sweden
    *Email: [email protected]
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    Orcidhttps://orcid.org/0000-0002-9720-5429
  • , and 
  • David González-Rodríguez*
    David González-Rodríguez
    Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
    Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
    *Email: [email protected]
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    Orcidhttps://orcid.org/0000-0002-2651-4566
Cite this: J. Am. Chem. Soc. 2023, 145, 32, 17805–17818
Publication Date (Web):August 2, 2023
https://doi.org/10.1021/jacs.3c04773

Copyright © 2022 The Authors. Published by American Chemical Society. This publication is licensed under

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Abstract

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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.

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Introduction

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Tubular nanostructures are a fascinating class of nano-objects that arise an extraordinary interest in materials science and biological chemistry. The structural and electronic applications of inorganic and carbon nanotubes have revolutionized the field of nanotechnology, (1) while the myriads of functions of biological micro- and nanotubules found in cells are essential to life. (2) Besides their high aspect ratio, certainly the most appealing feature of tubular structures is their well-defined internal nanochannels, which can be potentially used to host and transport molecules with high selectivity, as impressively demonstrated by many transmembrane proteins. (3,4)
Inspired by the structure and performance of these natural systems, chemists have developed numerous approaches to nanotubes based on the self-assembly of small molecules. (5,6) The use of amphiphilic molecules/block copolymers that aggregate in water through hydrophobic effects into cylindrical objects, instead of spherical vesicles, is certainly the simplest and most widely employed strategy when targeting relatively large tube cross sections (i.e., >10 nm). (7) Reaching inner pore diameters that are smaller and better defined, more compatible with molecular dimensions, requires other strategies that make use of more sophisticated molecules and directional noncovalent interactions. For instance, covalent macrocycles can be made to orderly stack on top of each other, often aided by peripheral H-bonding units, to form cylindrical structures with well-defined pores (Figure 1a, left). (8−14) Alternatively, relatively flexible linear oligomers can be made to fold intramolecularly into helical structures (i.e., foldamers; Figure 1a, right), (15) which can also present available internal channels.

Figure 1

Figure 1. (a,b) Strategies to nanotube self-assembly through (a) the stacking of cyclic molecules or the folding of linear polymers or (b) the supramolecular polymerization of a molecule with two terminal binding sites that is able to assemble into cyclic entities or folded oligomers. (c) Chemical structure of dinucleobase monomers GC and AU. (d) Self-assembly of GC/AU. Watson–Crick pairing between complementary G:C and A:U nucleobases affords a mixture of H-bonded oligomers in equilibrium, among which an unstrained cyclic tetramer may be significantly stabilized if chelate cooperativity is strong enough. Polymerization through π–π stacking interactions and H-bonding between peripheral amides may then take place from these macrocycles (top) or from folded conformations of the linear oligomers (bottom), resulting, respectively, in stacked or coiled polymer nanotubes.

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A drawback of employing these cyclic or linear oligomers for nanotube construction is that their covalent synthesis can be tedious and low-yielding. To circumvent this problem, diverse supramolecular strategies that can generate analogous architectures with lower synthetic effort have been explored. On one hand, supramolecular macrocycles (16,17) can be assembled through diverse noncovalent interactions to define the cyclic nanotube sections (Figure 1b, left). (18) For instance, H-bonded rosettes can be formed from molecules with suitable heterocyclic head groups, (19−24) while cyclic structures leading to larger internal tube volumes can be accessed through diverse strategies exploiting metal–ligand, (25) van der Waals, (26,27) and H-bonding interactions. (28) On the other hand, relatively short oligomers that are able to adopt helically folded conformations can also be extended via end-to-end noncovalent association into polymeric nanotubes (Figure 1b, right). (15,29,30)
In general, both of these supramolecular strategies rely on molecules with two noncovalent bindings sites or “sticky“ edges that undergo either intermolecular cyclization–stacking or folding–polymerization events, as shown in Figure 1b. A subtle interplay exists between these two aggregation pathways that largely depends on the structure of the monomeric molecule and on the binding interaction. Relatively flexible molecules/oligomers with some tendency to fold intramolecularly may prefer to yield helically coiled tubular structures, whereas rigid molecules with directional interactions that are able to generate unstrained cycles may opt to stack in the form of ring-shaped entities. At the same time, each of these pairs of events (i.e., cyclization+stacking and folding+polymerization) may be decoupled or coupled, meaning that the corresponding discrete supramolecular intermediate (i.e., macrocycle, folded conformer, etc.) may be detected or not prior to the completion of the aggregation process. In any case, for a monomer for which these two possible pathways are in principle available, it is difficult to predict and often to determine experimentally the kind of tubular architecture generated.
In this work, we provide an example that clearly demonstrates that the chosen pathway may largely depend on chelate cooperativity, that is, on the thermodynamic preference of a molecule to cyclize into a given ring size. Herein, we study in detail the self-assembly of two almost identical molecules (GC and AU; Figure 1c) having complementary nucleobases at their termini. We discovered that despite this structural resemblance, they assemble into supramolecular nanotubes through two rather distinct mechanisms depending on the cooperativity displayed toward the formation of a Watson–Crick H-bonded macrocycle. The molecule endowed with guanine (G) and cytosine (C) nucleobases (GC) enjoys high cyclization cooperativities that result in the formation of very robust cyclic tetramers (c(GC)4) prior to the stacking process. On the contrary, the same molecule with 2-aminoadenine (hereafter abbreviated as A) and uracil (U) complementary bases (AU) shows a weak tendency to cyclize into c(AU)4 tetramers and instead aggregates into linear polymers with folded conformations. Such distinct pathways result in tubular structures with identical diameters but opposite helicities, as experimentally demonstrated by circular dichroism (CD) and circularly polarized luminescence (CPL), and corroborated by a combination of molecular dynamics (MD) and density functional theory (DFT) calculations, and they are formed through distinct polymerization mechanisms with different nucleation-growth cooperativities.

Results and Discussion

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GC and AU: Two Dinucleobase Monomers with a Similar Structure but Showing Important Self-Assembly Differences

Dinucleobase derivatives GC and AU (Figure 1c) share a common structure designed to yield self-assembled nanotubes based on our own previous experience. (31−34) The complementary nucleobases were connected through a rigid and linear p-phenylene block attached at the purine 8- and pyrimidine 5-positions. In this way, association through Watson–Crick pairing provides a 90° angle between monomers, which can favor the formation of unstrained rectangular assemblies (i.e., c(GC)4 or c(AU)4 cyclic tetramers; Figure 1d). (35,36) Such π-conjugated central block was at the same time substituted with S-chiral tails, so as to bias the helical chirality of the final tubular assemblies. On the other hand, benzylic wedges substituted with long alkyl tails were installed at the N-9 and N-1 positions of the purine and pyrimidine bases, where the deoxyribose units are located in DNA, in order to enhance π–π stacking interactions along the nanotube axis and provide solubility to the final assemblies in organic solvents. In addition, a peripheral amide group was installed at the pyrimidine nucleobase, so as to guide stacking/folding by establishing H-bonding interactions parallel to the tube’s axis (see Figure 1). In short, the only structural difference between GC and AU molecules is the exchange of carbonyl and amino groups at the C-6 of purines and C-4 of pyrimidines (see Figure 1c), but all peripheral substituents and chiral groups are exactly the same. Synthetic and characterization details can be found in our previous work (for GC) (31) and in the S.I. accompanying this paper.
Both GC and AU compounds can be molecularly dissolved in their monomeric state in relatively polar solvents like THF at low concentrations. H-bonding through Watson–Crick interactions can be triggered at higher concentrations or by the addition of less polar (co)solvents, like CHCl3, toluene, cyclohexane, or heptane. The strength of such H-bonding interactions is greater and thus occurs at lower concentrations or in more polar solvents for the G:C pair than for the A:U pair. This is a well-known fact explained by the Jorgensen model of secondary interactions: (37) the DAD:ADA H-bonding pattern of the A:U pair affords lower association constants (K) than the DDA:AAD pattern of the G:C pair (i.e., in CHCl3: KG:C ∼ 2·104 M–1; KA:U ∼ 3·102 M–1), (38,39) despite both Watson–Crick pairs binding through three H-bond contacts.
Decreasing solvent polarity even further, by increasing the volume fraction of cyclohexane (Vcy) or heptane (Vhep) for instance, leads to higher degrees of aggregation due to an enhancement of the strength of π–π interactions between the π-conjugated segments on one hand and of H-bonding interactions between the peripheral amides purposely placed at the pyrimidine bases (C or U) on the other. Ultimately, in pure cyclohexane/heptane, we observed precipitation of the samples within the 10–3–10–7 M concentration range used in the spectroscopic measurements, which is an indication of the formation of large aggregates. Therefore, a small amount ≥1% v/v of a good solvent (preferably THF but also CHCl3) was always required to dissolve the aggregates formed by GC and AU in these apolar aliphatic environments. In this way, the whole self-assembly process could be monitored by moving from the monomer in THF to polymeric aggregates in cyclohexane-D12 (for 1H NMR measurements at 10–2–10–4 M) or heptane (for optical spectroscopy measurements at 10–4–10–6 M). Figure 2a–d,a′–d′, respectively, show the changes observed for GC and AU in 1H NMR, CD, absorption, and emission spectroscopy upon increasing Vcy/Vhep in THF:cyclohexane-D12/heptane mixtures. Figure 2e displays the CD trends recorded at a fixed wavelength along the whole Vhep sweep range. Further information and the corresponding spectra and curves at other concentrations can be found in the S.I. Careful inspection of the spectroscopic data recorded along the aggregation of GC and AU allowed us to remark the following differences:

Figure 2

Figure 2. Complete self-assembly of GC and AU. Self-assembly of GC (a–d) and AU (a′–d′) by progressively increasing the volume fraction of cyclohexane-D12 (Vcy; for 1H NMR studies) or heptane (Vhep) in mixtures with THF-D8 or THF, respectively, as monitored by (a,a′) 1H NMR at 5.0·10–4 M (please, see also Figure S1B), (b,b′) absorption, (c,c′) CD, or (d,d′) emission spectroscopies at 3.0·10–5 M. In the 1H NMR signal assignments, rod-shaped marks correspond to monomers or linear oligomeric species, while square-shaped marks correspond to cyclic tetramers. (e) Normalized CD changes at 429 nm at several concentrations as a function of Vhep for GC and AU at 298 K (αT = fraction of cyclotetramers, αN = fraction of nanotubes).

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(1) In contrast to c(GC)4, c(AU)4 cyclic tetramers were not detected by any experimental technique. Not only the strength of the intermolecular association but also the kind of Watson–Crick-bound oligomers obtained from such interactions differ for GC and AU compounds.
Monomer GC shows a strong tendency to cyclize into tetrameric rings, which display the typical Watson–Crick H-bonded G-amide and C-amine proton signals at ca. 13.5 and 10.0 ppm. As shown in Figures 2a and S1B, the 1H NMR spectra recorded for GC in THF-D8 at different Vcy values show an equilibrium between monomer GC and cyclic tetramer c(GC)4 in slow exchange at the NMR timescale, which is shifted to the macrocycle side as Vcy increases. The observation of this H-bonded species in slow NMR exchange is a solid proof for the formation of c(GC)4, as determined in our previous work. (31) A similar picture is clearly observed in variable temperature experiments in THF-D8 (Figure S1A), where the whole transition from the GC monomer at high temperatures to the c(GC)4 cyclic tetramer at low temperatures can be monitored. At higher amounts of Vcy, the c(GC)4 signals broaden and eventually vanish due to, as will be explained below, supramolecular polymerization (bottom NMR spectra in Figure 2a).
However, in the same conditions, AU just shows a single set of proton signals along the whole Vcy (Figures 2a′ and S1B) or temperature (Figures S1A and S1C) sweep range. The H-bonded A and U proton signals, the latter found within the 14–10 ppm window, shift downfield upon increasing Vcy or decreasing T due to their higher involvement in H-bonded species in fast NMR exchange, but a cyclic species in slow exchange is not detected in any of the experiments performed as a function of solvent, temperature, or concentration. Just like for GC, at very high Vcy, the AU signals broaden and then disappear due to polymeric aggregation.
These qualitative observations are in agreement with previous studies with related G-C and A-U dinucleosides substituted with bulky lipophilic ribose groups, so as to prevent stacking interactions, (35,36) which disclosed chelate cooperativities in their cyclotetramerization processes that can be 5 to 8 orders of magnitude higher for c(G-C)4 than for c(A-U)4. Since chelate cooperativity is quantified by the product K·EM, where EM stands for effective molarity, one of the reasons stems of course from the mentioned fact that the association constant K of the G:C pair is stronger than the A:U pair. However, another, even more important difference comes from the magnitude of the EM associated to the cyclization process. EM values were calculated as high as 102–103 M for the c(G-C)4 rings, which is an extraordinarily high value for cyclic assemblies. (40) As a result, these kind of systems have been employed by us for manifold purposes: to study in detail chelate cooperativity, (41−43) to self-sort fluorescent dyes, (44,45) to produce 2D networks with well-defined nanocavities, (46) or to efficiently disperse carbon nanotubes through a clasping mechanism. (47) On the contrary, EM values as low as 10–2–10–3 M have been calculated for c(A-U)4 macrocycles. (36) This huge difference, that spans over 4–6 orders of magnitude, was ascribed to entropic effects related to the number of degrees of freedom that are lost upon cyclization, depending on the symmetric (DAD:ADA) or unsymmetric (DDA:AAD) nature of H-bonding pattern between nucleobases (for further details, please see our previous work). (36) For the systems studied in the current work, an EM value of 1.2·102 M was calculated for c(GC)4 in THF. (32) On the other hand, a higher EM limit of 10–2 M was estimated for c(AU)4, when compared to other A-U dinucleosides studied by us, (36) but this value is probably considerably lower in view of the impossibility to detect this species even in solvents of low polarity.
(2) GC and AU displayed, respectively, 2-step and 1-step self-assembly processes. In line with these NMR results and as noted in the spectra and curves respectively shown in Figure 2b–e, GC displays two transitions with clear isosbestic points in the whole Vhep range. The first one, found between Vhep ∼ 0 and 0.5 (at ca. 10–4–10–5 M), corresponds to the cyclotetramerization process. Then, a plateau is reached between ca. Vhep ∼ 0.5 and 0.9 where this highly stable c(GC)4 macrocycle becomes the dominant supramolecular species, and then, above Vhep ∼ 0.9, a supramolecular polymerization process is triggered. In sharp contrast, when inspecting the behavior of AU under the same conditions (Figure 2b′,d′,e; see also Figures S2A–B), a single transition above Vhep ∼ 0.8 attributed to a polymerization process is recorded by all techniques, and no distinct self-assembled intermediates are detected at lower polarities, which is in line with the observations made in the previous point.
A quite remarkable difference in the self-assembly of both monomers was also seen in aromatic solvents. In toluene, GC formed very robust c(GC)4 cyclic tetramers that can persist even at high temperatures at relatively low concentrations (see Figures S1C and S2G, for example). (31) However, these macrocycles did not polymerize in this solvent even at NMR concentrations, in the mM range (see Figure S1C) and required the addition of an alkane cosolvent to induce stacking interactions. In sharp contrast, AU was seen to undergo the complete polymerization process in 100% toluene within the 5–80 °C range above 10–4 M (see Figures S1C and S2H). The isosbestic points and spectral features recorded by decreasing temperature in toluene match those seen by increasing Vhep in THF:heptane mixtures: the relevant H-bonded protons shift downfield and then they broaden and disappear (Figure S1C), absorption is red-shifted, fluorescence emission is considerably quenched, and a negative Cotton effect arises (please compare Figures S2F and S2H). Further details about the distinctive self-assembly of these molecules and their mixtures in toluene will be shown below.
(3) AU exhibited a much stronger aggregation tendency but lower nucleation-growth cooperativities than GC. The supramolecular polymerization/depolymerization transitions of GC and AU were recorded in both solvent- and temperature-dependent experiments and analyzed by their corresponding mathematical models (see S.I. Section S2 for details). The degree of cooperativity (σ), defined as the ratio between the nucleation and elongation equilibrium constants (σ = Kn/Ke), was calculated and compared for these two molecules. From the denaturation curves as a function of solvent composition at different overall concentrations, obtained by increasing the volume fraction of THF (VTHF) in mixtures with heptane, moderate and comparable σ values in the order of 10–1 (Figures 3a and S2B and Table S1) were obtained for both molecules. An additional observation obtained from these experiments is that the polymerization of AU occurs at considerably lower heptane contents than the polymerization of GC, which is sequestered as c(GC)4 cycles, at the same concentration (see Figures 2e or 3a).

Figure 3

Figure 3. Spectroscopic and morphological differences in the self-assembly of GC and AU. (a, b) CD trends recorded at 429 nm (GC) or 430 nm (AU) as a function of (a) the volume fraction of THF (VTHF = 1 – Vhep) in THF:heptane mixtures at 298 K or (b) the temperature in THF:heptane mixtures at Vhep = 0.97 ([GC] = 3.0·10–5 M (orange squares); [AU] = 8.0·10–6 M (green triangles)) or Vhep = 0.90 ([AU] = 3.0·10–5 M (green squares)). (c) Absorption, (d) emission, (e) CD, and (f) CPL spectra of the (GC)n and (AU)n polymers (solid lines) at Vhep = 0.99 compared to the GC and AU monomers (dashed lines) at Vhep = 0. (g, h) TEM images of the assemblies formed by (g) GC and (h) AU drop-cast from diluted solutions of high Vhep. (i) Nanotube diameter distributions measured by TEM.

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Experiments carried out at a fixed solvent composition (Figures 3b and S2D–I), in which temperature is varied at low rates with <0.1 K accuracy and a global fitting can be made from measurements at different concentrations, are generally preferred for a precise thermodynamic control of the nucleation and elongation events and to supply more accurate and reliable thermodynamic parameters. (48−52) Once again and as shown in Figure 3b, the propensity of AU to aggregate in polymeric tubes was observed to be much higher in the same solvent conditions than that of GC (or, more exactly, c(GC)4). For instance, at the same concentration (3.0·10–5 M) AU and GC required 10:90 and 3:97 THF–heptane solvent mixtures, respectively, to record the whole polymerization process within our experimental temperature window. Likewise, in the same 3:97 THF–heptane solvent mixture, the elongation temperature (Te) determined for AU was more than 50 K higher than the one measured for GC, even if the concentration of the former compound had to be decreased from 3.0·10–5 M to 8.0·10–6 M to detect the nucleation event (see Figures 3b and S2D,E). Unfortunately, the cyclotetramerization and the polymerization events of GC occur within very different experimental windows and, due to technical limitations, we could not monitor both processes consecutively as a function of the temperature in a single solvent system (like we did in the solvent-dependent experiments).
Moreover, in these temperature-dependent experiments, we observed some marked differences in the cooperative polymerization of both molecules, as graphically revealed in Figure 3b. The polymerizations of GC enjoyed higher cooperativities (σ = 3.0·10–4 at Vhep = 0.97) than those of AU (σ = 1.0·10–2 at Vhep = 0.97, σ = 2.6·10–1 at Vhep = 0.90 and σ = 1.1·10–1 in toluene), as shown in Figure S2I and Table S2. Both compounds displayed at Vhep = 0.97 with similar equilibrium constants for the elongation phase (Ke GC = 1.3·105; Ke AU = 1.8·105), and the differences in cooperativity stem from a smaller equilibrium constant of the nucleation stage (Kn GC = 4.0·101; Kn AU = 1.8·103).
In all of these solvent- or temperature-dependent experiments, we made sure that we worked under equilibrium conditions and that the observed deviations are not caused by time or solvent effects. The final spectroscopic features did not evolve with time or thermal annealing, and cooling and heating curves converting the monomer into the aggregate and vice versa perfectly overlapped at various concentrations and solvents (see Figures S2F and S2H).
(4) Despite their virtually identical structure, GC and AU molecules displayed quite different aggregate spectroscopic features. A final, but most remarkable difference between the supramolecular polymers of GC and AU comes from the analysis of their basic spectroscopic characteristics. As already noted, the final absorption, emission, and CD spectra of (GC)n and (AU)n polymeric aggregates is considerably different. For the sake of comparison, we display the absorption, emission, CD, and CPL spectra for both compounds in their monomeric (Vhep = 0) and polymeric (Vhep = 0.99) form in Figure 3c–f (see also Figure S2C). First of all, both molecules develop a red-shifted absorption band upon polymerization (Figure 3c), but the one disclosed by AU is significantly more pronounced and shifted (Δλ = 12 nm) than the one of GC (Δλ = 6 nm). On the other hand, both molecules experience a significant decrease in emission intensity (83% quenching for GC and 87% for AU; Figure 3d) and a notable red shift in emission maxima when comparing polymer and monomer samples, but this shift is now smaller for AU (Δλ = 36 nm) than for GC (Δλ = 75 nm). It is important to remark, as can be appreciated in Figure 2b–d, that the cyclotetramerization process experienced by GC, just like all G-C dinucleosides studied by the group (please, see our previous work), (40) already brings about important spectroscopic changes that are attributed to the loss of degrees of freedom and planarization of the π-conjugated phenylene–ethynylene system. For instance, fluorescence emission is quenched and red-shifted upon cyclization (red to green lines in Figure 2d), whereas stacking of these cyclotetramers into polymeric tubes results in a further reduction of fluorescence emission and a slight blue shift (green to blue lines in Figure 2d).
Nevertheless, the spectroscopic differences between (GC)n and (AU)n polymers are even more pronounced in the CD and CPL spectra in THF:heptane solutions at Vhep = 0.99. As shown in the CD spectra in Figure 3e, (AU)n polymers display a negative Cotton effect with maxima at 333(+), 394(+), and 433(−) nm, whereas (GC)n polymers show a positive Cotton effect with maxima at 341(−), 402(−), and 440(+) nm. On the other hand, Figures 3f and S2K,L show the CPL spectra of (GC)n and (AU)n. In both cases, the CPL band is in correspondence with the high energy side of the fluorescent feature, and this is particularly evident for (AU)n, which presents a blue shift of about 25 nm. The CPL sign is the same as the sign for the lowest-energy CD band, as expected and observed in most cases, so the information about the opposite chiral helicities can be obtained both through CD and/or CPL. Indeed, comparing (GC)n and (AU)n, they display almost, but not exactly (due to an evident wavelength shift), mirror image CD and CPL features, despite bearing the same S-chiral center (Figure 3e,f). In line with all other spectroscopic techniques, the CPL spectrum recorded for (AU)n in toluene (Figure S2L) is similar, although slightly more intense, to the one found in THF:heptane. Furthermore, one may notice that, in toluene, CPL and fluorescence bands are centered at the same wavelength.
In short, we would like to emphasize that the chiroptical response of (GC)n and (AU)n nanotubes are almost a mirror image but not exactly due to the differences noted in absorption and emission maxima. This suggests that the differences in the internal organization of each dinucleobase molecule in the polymeric aggregates must also go beyond a simple mirror image relationship.
On the other hand, the CPL spectra observed for the two aggregation states of GC (c(GC)4 and (GC)n), measured, respectively, at Vhep = 0.40 and Vhep = 0.99, are quite similar in shape and wavelength (see Figure S2K). The only difference comes from a decrease of the CPL signal from c(GC)4 to (GC)n, which is different from the changes observed in the CD spectra (see Figure 2c). However, we should consider that CPL originates from the lowest energy transition, while several transitions contribute to CD and may partially cancel each other.
(5) Both GC and AU form self-assembled nanotubes with similar diameters that coincide with a tetrameric cross section. Dried samples drop-cast from solvent mixtures at high Vhep were analyzed by means of scanning and transmission electron microscopy (SEM and TEM) experiments, so as to compare the morphology and dimensions of the final aggregates formed by GC and AU molecules. A general conclusion from all microscopy experiments performed is that the nanotubes formed by both dinucleobase compounds displayed a large tendency to bundle in solution and that the longer the time before deposition, the higher the degree of nanotube bundling. As a matter of fact, when GC or AU was left for several days in solutions of high Vhep, a precipitate emerged, especially in concentrated samples. Bundling was beneficial for a successful detection of the nanotubes onto the grid but detrimental for the study of isolated nanotubes. The best electron microscopy images were obtained when the solution was prepared 2–3 days before deposition. SEM measurements of Cu-metallized samples deposited onto glass substrates (Figures S3A–B), as well as low-voltage TEM measurements carried out on stained samples (Figures S3C–D), revealed the formation of dense networks of large longitudinal entangled aggregates, but the diameter of the individual constituents could not be determined. Working at higher voltages with nonstained samples deposited onto copper grids coated with carbon, conditions that provided higher contrast and resolution, allowed us in contrast to image individual (GC)n and (AU)n nanotubes, as shown in Figures 3g,h and S3C–D.
The analysis of multiple TEM images (Figure 3i) afforded a mean nanotube diameter of 3.9 ± 0.7 nm for (GC)n, dimensions that are in agreement with previous SAXS and DLS measurements (31) and that match the aromatic hard section of the c(GC)4 cyclic tetramers. For the (AU)n nanotubes, a slightly narrower mean diameter of 3.8 ± 0.4 nm was calculated. Aside from these minor differences, the dimensions of the nanotubes formed by GC and AU dinucleobase molecules were virtually indistinguishable, and their internal stacked/folded helical structure could not be elucidated by means of any microscopy technique we utilized in this work. This included the use of aberration-corrected high-resolution TEM techniques, which unfortunately resulted in rapid nanotube decomposition under the high-power electron beam.

GC and AU Narcissistically Self-Sort along Their Self-Assembly Processes

Points 1–3 above support the notion that the overall aggregation mechanism diverges for S-chiral dinucleobase molecules GC and AU, despite their almost identical structure. The first difference comes at the early stages of the aggregation process, where GC fully associates in cyclic species, which are nonetheless not detected for AU. However, one might argue that most examples of nanotube aggregation from molecules forming, for instance, H-bonded rosette-type assemblies also occur without the detection of cyclic intermediates, (19−24) so this could just be the same case. This means that, as soon as small (nondetected) amounts of c(AU)4 cyclic species are formed in solution, they may act as (pre)nuclei for the coexisting monomer and short H-bonded oligomers to trigger polymerization. In other words, cyclotetramerization and polymerization would be decoupled for GC due to the extraordinary stability of the c(GC)4 macrocycles but could be strongly coupled for AU. However, if this was the case, we would expect that both final (AU)n and (GC)n polymer products, both composed of comparable stacked macrocycles, should show similar spectroscopic properties. Although the images recorded by TEM, as disclosed in point 5 above, reveal nanostructures of matching morphology and diameter for (AU)n and (GC)n, the spectroscopic observations exposed in point 4 clearly show that the internal structure of each final nanotube is markedly different. Moreover, as noted in point 3, AU reveals a notably stronger propensity to polymerize than GC, although with poorer cooperativity, which also disagrees with the idea that tiny amounts of c(AU)4 could act as nucleation seeds for polymerization.
In order to fully discard the fact that the polymerization of AU does not proceed via stacking of c(AU)4 macrocycles, we carried out self-sorting experiments (53−57) (Figure 4) by mixing both GC and AU molecules. We know from recent studies that a strong narcissistic self-sorting process operates along the cyclotetramerization of these kinds of dinucleobase monomers, which is mainly driven by a strong chelate cooperativity, in addition to the different complementary H-bonding patterns of the G:C and A:U pairs. (45) However, the supramolecular picture during polymerization may be very different. We hypothesized that if AU polymerized in the form of c(AU)4 cycles and/or required nuclei formed by such cyclic entities, then c(AU)4 and c(GC)4 should costack along polymerization, thus leading to statistically mixed assemblies. In other words, we would expect the absence of self-sorting effects during the polymerization of c(AU)4 and c(GC)4 macrocycles due to their strong structural resemblance and to the fact that they are endowed with exactly the same peripheral groups and chiral tails.

Figure 4

Figure 4. Self-sorting experiments. (a) Self-assembly of a 1:1 mixture of GC + AU by progressively increasing the volume fraction of cyclohexane-D12 (Vcy) in mixtures with THF-D8 monitored by 1H NMR ([GC] = [AU] = 2.0·10–3 M; T = 298 K; see also Figures S4A). The pictures at the right indicate approximately the distribution of supramolecular GC and AU species as Vcy is increased. Please compare with Figure 2, where the individual evolution of GC and AU is displayed. (b) Self-assembly of a 1:1 mixture of GC + AU by progressively increasing the volume fraction of heptane (Vhep) in mixtures with THF monitored by CD ([GC] = [AU] = 1.5·10–4 M; T = 298 K; see also Figures S4B). (c) Normalized CD changes at 435 nm as a function of Vhep for GC, AU, their mixture (spectra shown in panel (b)), and the arithmetic sum of GC+AU CD intensity taken from the isolated samples (αT = fraction of cyclotetramers, αN = fraction of nanotubes). (d) Self-assembly of a 1:3 mixture of GC + AU monitored by emission spectroscopy by progressively decreasing temperature in a THF:heptane mixture at Vhep = 0.9 ([GC] = 1.0·10–5 M; [AU] = 3.0·10–5 M; see also Figures S4C). (e) Normalized emission changes at 450 nm as a function of T for GC, AU, their mixture (spectra shown panel (d)), and the arithmetic sum of GC+AU emission intensity taken from the isolated samples.

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Thus, from all of the data gathered so far, we planned a set of experiments that could discern if the aggregation pathways of GC and AU are independent or if, on the other hand, these molecules mix in the polymeric assemblies. This is not trivial, in view of the identical absorption and emission windows of these two chromophores and the related experimental conditions under which they polymerize. However, by playing with relative monomer concentration and solvent composition, we were able to find conditions in which we could (1) scan the whole aggregation landscape and record consecutively GC cyclotetramerization, AU polymerization, and c(GC)4 polymerization and (2) monitor AU polymerization in the presence of c(GC)4 macrocycles.
The first case was realized by increasing Vcy/Vhep in THF:cyclohexane-D12/heptane mixtures, and could be respectively monitored by 1H NMR and by optical spectroscopy under experimental conditions that are similar to those shown in Figure 2. In the 1H NMR experiments, as shown in Figures 4a and S4A, our starting situation at Vcy = 0 and 2.0·10–3 M concentration in each compound (top spectrum) reveals a mixture of dissociated AU and GC monomers. By gradually increasing Vcy, we basically observe the same changes shown independently by each compound (Figure 2): the H-bonding protons of AU experience a downfield shift that indicates the formation of a fast exchanging mixture of H-bonded oligomers, whereas the c(GC)4 proton signals appear and increase in intensity at the expense of the GC monomer signals. Further decrease in solvent polarity within the 0.3 < Vcy < 0.7 range kept downshifting the H-bonded proton signals of AU, indicating the formation of larger oligomers, while the c(GC)4 signals remained unchanged. Above Vcy > 0.75, the AU proton signals begin to broaden significantly and then disappear, indicating the formation of polymer nanotubes. In the 0.75 < Vcy < 0.85 solvent composition window, the (AU)n polymers and c(GC)4 macrocycles coexist, but the supramolecular behavior of each species does not seem to influence the other. Finally, above Vcy > 0.85, the c(GC)4 signals start to broaden and then disappear, revealing the polymerization of this species as well.
While these NMR experiments are very clear and highly informative, a quantitative comparison between the supramolecular behavior of S-chiral AU and GC molecules when isolated and in mixtures could be more accurately obtained from optical spectroscopy experiments and in particular from CD and emission spectroscopy due to the distinct signatures of c(GC)4, (GC)n, and (AU)n (see Figures 2 and 3). A screening of multiple concentrations and [GC]/[AU] ratios allowed us to choose [GC] = [AU] = 1.5·10–4 M as the best conditions to record consecutively all self-assembly processes by increasing Vhep in THF/heptane mixtures. As revealed in Figures 4b,c and S4B, the cyclotetramerization process of GC is first monitored within the Vhep = 0–0.3 range. Then, the polymerization of each compound is monitored successively at higher Vhep values: AU polymerizes first at Vhep > 0.8, while (GC)n polymerization is activated just after Vhep > 0.9. Interestingly, the trends observed for the supramolecular processes of S-AU and S-GC in these mixtures match quite reasonably those seen by the same molecules independently (see Figures 4c and S4B), suggesting again a narcissistic self-sorting behavior.
Inferring from the presented spectroscopic data, one might argue that the reason behind the opposite chirality of (AU)n with respect to (GC)n might reside in that the fragile c(AU)4 species also presents opposite chiral with regards to c(GC)4. In this scenario, the clear independent aggregation pathways observed in the GC+AU mixtures could be originated from chiral self-sorting, which has been demonstrated to play a crucial role in self-assembly. (58−62) We believe this is an improbable situation since GC and AU share the same S-chiral groups and because the most strikingly different feature in the polymerization of AU is not the opposite CD sign generated but probably its much stronger predisposition to polymerize, compared to GC, even if the c(AU)4 species is far less stabilized. In any case, in order to discard chiral self-sorting events, the same solvent-dependent experiments shown in Figure 4c,d by mixing S-GC and S-AU were now performed by mixing R-GC (31) and S-AU molecules under the same conditions. The results, shown in Figure S4C, reveal the same strong narcissistic self-sorting process with almost identical transitions for the heterochiral and the homochiral mixtures, thus discarding the existence of chiral self-sorting mechanisms that would generate (AU)n from oppositely chiral c(AU)4 macrocycles.
Lastly, the robustness of the c(GC)4 macrocycle enabled us to explore several conditions in which AU polymerization can be recorded as a function of the temperature in the presence of this cyclic species. This can be done, for instance, using THF:heptane mixtures at Vhep = 0.9 and [GC] = 1.0·10–5 M and [AU] = 3.0·10–5 M concentrations. As displayed in Figures 4d,e and S4D using fluorescence emission, a temperature variation between 373 and 263 K does not affect significantly the integrity of the c(GC)4 cycle in this solvent environment, while the whole AU polymerization process is recorded. The same conclusion was derived by monitoring the aggregation processes of AU + GC mixtures by CD spectroscopy in toluene (Figure S4E), a solvent in which, as noted above, AU polymerizes but not GC, which remains sequestered as c(GC)4 cycles even at low temperatures and/or high concentrations. Once again, the fact that AU polymerization follows the same transitions without or with comparable amounts of the GC molecule confirms that these molecules self-sort narcissistically forming their own aggregates.

Simulations of Supramolecular Structures and Spectra

To reveal and analyze the underlying microscopic reasons for the different spectroscopic features of the supramolecular assemblies of GC and AU, we performed molecular dynamics (MD) simulations of the respective nanotube formations. We adopted a bottom-up approach and started by performing a study of the structure and conformational preferences of the monomers in a bulk solvent (99% heptane and 1% THF), as shown in Figures S5A,5B and Table S3. Next, we studied the adopted assemblies in small stacked cyclic systems. We prepared models of c(GC)4 and c(AU)4 by arranging four monomers into squares and placing them on top of each other in two layers (2SQ) or eight layers (8SQ). The 2SQ simulations showed that GC preferred to stay in the form of two separate squares (Figure S5C). In the case of AU, on the other hand, the squares did not stay intact but instead broke and finally all eight monomers were interconnected in helix-like structures. A similar observation was valid also for the 8SQ systems (Figure S5D and Table S4): we observed stable squares in the case of GC but the disruption of several squares and the formation of a helix in the case of AU.
Based on the 8SQ systems, we built larger assemblies, resulting in simulations of infinite nanotubes with periodic boundary conditions (for details, see SI Section S5.2.3). Building and simulating periodic GC and AU nanotubes resulted in stable systems with different twists and geometries. Short segments of these helical structures are illustrated in Figure 5, where selected nitrogen atoms in the nucleobases are depicted as spheres to better appreciate the helicity. Macroscopically, both GC and AU formed nanotubes with a diameter of about 3–4 nm, considering the rigid core, and about 7–8 nm, including the peripheral chains (Figure S5I), which agrees with the TEM analyses. Microscopically, however, we observed some differences between these two systems. The squared intact GC system was more compact, showing an interlayer π-stacking distance of 0.36 nm (Figure S5H). In contrast, the layers in the AU system were interconnected in a spiraling structure and separated by a π-stacking distance of 0.40 nm (Figure S5F). Both systems were able to establish stabilizing H-bonds between peripheral amides, although the average number of these amide–amide bonds was slightly higher for the AU nanotube (Table S5). However, the overall number of H-bonds in the GC nanotube is higher (15.6 per four molecules) than that in AU (14.3, Table S5). This difference does not come from base pairing or peripheral amide–amide interactions but mostly from the contribution of H-bonds between side chain oxygens and the exocyclic amine groups of purines, which are more abundant for guanine (Figure S5J). Also, the mutual orientation of GC molecules was mostly square-like (∼90° between the residues), whereas AU edges were not so regular, corresponding to an overall helix organization (Figure S5L). We believe that the different orientations originate from the different preferential monomer conformations (Figure S5B). We also observed that while the GC molecules preferred a planar conformation, the AU molecules were mostly rotated and therefore preferred a helical reorganization (Figures 5 and S5L).

Figure 5

Figure 5. Simulations of supramolecular structures and spectra. Final structures of GC and AU nanotube models with molecular cores shown in magenta, A and G nitrogens in blue, and side chains as semitransparent green sticks. The nanotube models have opposite twist. The insets show the details of the nanotube core conformation. At each side, the CD spectra calculated as ensemble average over 10 snapshots extracted from the MD simulations is shown. The thin vertical lines show rotatory strengths from individual excited states. Units are arbitrary but comparable in between the two systems.

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Finally, we put the supramolecular model structures to test by calculating the associated CD spectra and compare them against the experimental results. In our experience, (63−68) CD spectra are very sensitive to the (supra)molecular structure and even a successful qualitative comparison between theoretical and experimental spectra can provide strong evidence for the structure model to be sound. Supramolecular systems in general, and our nanotubes are no exception to this rule, are sufficiently dynamic at room temperature to mandate a configuration space sampling when performing CD spectrum simulations. Therefore, we extracted 10 snapshots from the MD simulations of the periodic GC and AU systems and calculated the associated ensemble averaged CD spectra with use of an exciton coupling model that took four nanotube layers into account. The decision to use four layers in the calculation was made after performing a large-scale benchmark calculation for a 10-layer system (Figure S5M). The calculated CD spectra confirmed the relevance of the presented model, as their shapes were in full agreement with experimentally observed CD spectra (compare Figures 3 and 5). In the case of the AU system, the procedure of ensemble averaging turned out to be of vital importance as several of the individual spectra showed to qualitatively differ from the averaged one (Figure S5O). In the case of the GC system, on the other hand, the individual spectra were in close agreement, which, in turn, resulted in an averaged CD spectrum of higher intensity compared to AU (Figure S5N). The trace origin of the CD signal turned out not to be the π-stacked nucleobases but rather the central phenylene cores bearing the chiral tails. This could be established after performing spectrum simulations for a system where the nucleobases had been removed and which showed a preserved band shape (Figures S5P and S5Q). As far as the CD responses are concerned, the role of the nucleobases is thus to dictate the formation of the supramolecular structure of the nanotubes and thereby also the 3D orientation of the central cores, which in turn give rise to the characteristic bands by means of induced CD though the effect of the exciton coupling mechanism.
In short, theoretical simulations, combining MD and DFT calculations, are able to explain the differences in the CD spectrum of (AU)n and (GC)n nanotubes from structural preferences of these dinucleobase molecules upon self-assembly at the nanoscale: while GC tends to associate in planar squares that stack in a right-handed helical organization, AU forms oligomers that fold into a spiral with a left-handed helical twist.

Impact of Chelate Cooperativity on the Aggregation Process

In view of all experimental data exposed so far, our own experience with dinucleoside macrocycles, and the revealing picture derived from computational studies, we propose a scenario in which (GC)n and (AU)n tubular polymers grow with very different mechanisms that ultimately lead to similar nanomorphologies, though different internal structures. In order to understand the pathway that each of these molecules take prior to polymerization, we are showing in Figure 6 diverse “supramolecular scenes” along the aggregation process of GC (top) and AU (bottom) that would be obtained as we enhance, from left to right, the degree of association by, for instance, increasing the volume fraction of apolar solvent (Vhep) or decreasing temperature (T). Higher Vhep or lower T values lead in general to stronger interactions between molecules and, in particular, before polymerization takes place, to larger Watson–Crick H-bonding association constants for both G:C and A:U pairs. In order to simulate the “scenes” before polymerization, we built speciation curves that show the distribution of H-bonded species (from the GC/AU monomer (in red) to linear oligomers up to the decamer (GC)10/(AU)10 (in blue), including c(GC)4/c(AU)4 cyclic tetramers (in green)) as a function of concentration. The two variables employed to build these profiles are the association constant between nucleobases (KG:C and KA:U) and the effective molarities for cyclotetramerization (EMGC and EMAU). We started with the association constants calculated in THF at 298 K (KG:C = 4.1·102 M–1 (32) and KA:U = 1.7·101 M–1), and then, these values were progressively increased from left to right, thus simulating the effect of having higher Vhep or a decrease in T. On the other hand, EM values were kept constant along the whole association process since this parameter does not vary strongly with solvent composition. (35,69) We thus employed the calculated EM value for c(GC)4 in THF (EMGC = 1.2·102 M), and an estimated value for c(AU)4 (EMAU = 5·10–4 M), as explained above. The shadowed areas shown in each distribution profile correspond to the experimental concentration range employed in the 1H NMR (ca. 10–2–10–4 M; in light orange) and optical spectroscopy (ca. 10–3–10–5 M; in light violet) experiments. As it can be appreciated in Figure 6 by comparison of top and bottom horizontal panels, two very different supramolecular evolutions are obtained for GC and AU preceding the polymerization event.

Figure 6

Figure 6. Impact of chelate cooperativity on the self-assembly pathway and nanotube structure. Schematic representation of the whole supramolecular self-assembly process leading to nanotubes with the proposed stacked or folded internal structures. We simulate here the supramolecular scenarios encountered by GC (top panel) or AU (bottom panel) as Vhep is increased in THF:heptane mixtures and hence the intermolecular association strength, when going from left to right. In the middle, a simplified version of the panel shown in Figure 2e is reproduced, which shows the experimental evolution of the GC cyclotetramerization, AU polymerization, and GC polymerization with increasing Vhep. Each of the dashed frameworks at the top and the bottom provides a “snapshot” of the distribution of supramolecular species present in solution at 4 selected Vhep ranges before polymerization is triggered. Each of these frameworks contains the corresponding speciation curves in which the distribution of Watson–Crick H-bonded oligomers, which includes open oligomers from the dimer to the decamer (in blue), the cyclic tetramer (in green), and the monomer (in red), is simulated as a function of the total concentration. Orange and purple bands indicate, respectively, the concentration range employed in the 1H NMR and optical spectroscopy experiments performed in this work. Chelate cooperativity is several orders of magnitude higher for c(GC)4 than for c(AU)4. As a result, GC undergoes an “all-or-nothing” association process in which the cyclic tetramer is in equilibrium with the monomer, while AU mostly self-associates in a mixture of open (non-cyclic) species. As Vhep increases from left to right, the population of Watson–Crick H-bonded species increases until polymerization can be triggered at very high heptane contents (Vhep > 0.8). At this point, the c(GC)4 macrocycles are formed quantitatively in solution, whereas AU oligomers are long enough to become stabilized through folding interactions. Polymers originating from these two different situations can have a tubular structure with stacked or coiled molecular arrangements.

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For GC (top panel), EM values are extraordinarily large and the association between G:C pairs is relatively strong, which leads to a very strong chelate cooperativity and to an “all-or-nothing” situation: either a robust cyclic tetramer is formed or nothing else but the monomer survives in solution, so the participation of open G:C H-bonded oligomers is insignificant. As KG:C is increased at higher Vhep/lower T, the c(GC)4 population increases until this ring is formed quantitatively, as also evidenced experimentally. If polymerization is triggered at this point, the corresponding nuclei would be formed by stacked cyclic tetramers and the polymer is fed from these very stable, both thermodynamically and kinetically, macrocycles. This scenario would lead to stacked polymer nanotubes. This organization, as theory suggests, can reliably reproduce the experimental CD spectrum recorded for (GC)n.
For AU (bottom panel), on the contrary, EM values are more than 4 orders of magnitude smaller, whereas KA:U is also significantly lower, which leads to a weak chelate cooperativity. Hence, as we increase KA:U at higher Vhep/lower T, open A:U H-bonded oligomers compete strongly with the c(AU)4 cyclic tetramer, and the latter is only formed in small amounts. Together with the AU monomer, these open oligomers are not active in CD nor provide 1H NMR signals in slow exchange, but their formation was experimentally proven by the downfield shift experienced by the relevant H-bonded 1H NMR probes. As we further increase Vhep/decrease T, the population of relatively long A:U bound oligomers becomes larger. We thus assume that these oligomers might be able to adopt folded conformations, aided by additional π–π stacking and H-bonding interactions between peripheral amides. Please note that this extra stabilization enjoyed by folded oligomers is however not considered in the simulations of the speciation curves. Some of these stabilized folded species may then grow by incorporation of more AU, thus shifting all equilibria toward the formation of folded or coiled polymer nanotubes before cyclic species are even formed in significant amounts.

Conclusions

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We provided here an example of two structurally related molecules that exhibit very different noncovalent association scenarios prior to their supramolecular polymerization and, as a result, generate self-assembled nanotubes with distinct monomer arrangements: either stacked or coiled. These internal structures can, at the same time, define different helicities that result in opposite chiroptical properties, as determined by CD and CPL.
The molecules comprise a S-chiral π-conjugated central block substituted with complementary nucleobases at its termini: either guanine and cytosine (GC) or 2-aminoadenine and uracil (AU). The establishment of Watson–Crick interactions between the edges of these monomers led to a distribution of H-bonded oligomers among which a cyclic tetramer stands out as a significantly stabilized species, as long as chelate cooperativity is high enough. Such high cyclization cooperativities are attained by the GC monomer, which can quantitatively form cyclic tetramers, but not by the AU monomer, which instead associates preferentially in open oligomers. The evolution of these two distinct supramolecular scenarios as the association strength is increased by, for instance, increasing the volume fraction of apolar solvent can offer a solid explanation of the pathway, followed by each dinucleobase monomer to arrive to stacked or folded nanotubes. However, it must be remarked that we have also demonstrated that the final (GC)n and (AU)n aggregates do not show any further transformation under any conditions, meaning that the stacked or folded organizations are not kinetic intermediates, but actually thermodynamic products. Computational simulations strongly support this notion, and clearly show the resilience of GC to maintain the cyclic assemblies, and the tendency of AU to disrupt them and instead develop coiled structures. Therefore, the entropic factors that rule chelate cooperativity in these systems and hence the preference to associate as cyclic species (please, see our previous work) must also operate when the molecules aggregate in the final nanotube assemblies and make them remain associated as stacked macrocycles or as polymeric spirals. The results and main findings of this work can be helpful in the design of novel strategies aiming to control the structure and the function of synthetic self-assembled nanotubes that can mimic biological analogues.

Supporting Information

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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.3c04773.

  • Experimental procedures and compound characterization data, along with the supramolecular study by 1H NMR, supramolecular study by optical spectroscopy, microscopy characterization of the self-assembled nanotubes, self-sorting experiments, and theoretical calculations (Figures S1–S5) (PDF)

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Author Information

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  • Corresponding Authors
    • Mathieu Linares - Laboratory of Organic Electronics and Scientific Visualization Group, ITN, Campus Norrköping; Swedish e-Science Research Centre (SeRC), Linköping University, 58183 Linköping, Sweden;  Orcidhttps://orcid.org/0000-0002-9720-5429;  Email: [email protected]
    • David González-Rodríguez - Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain;  Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain;  Orcidhttps://orcid.org/0000-0002-2651-4566;  Email: [email protected]
  • Authors
    • Marina González-Sánchez - Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain;  Orcidhttps://orcid.org/0000-0002-2292-0794
    • María J. Mayoral - Department of Inorganic Chemistry, Universidad Complutense de Madrid, 28040 Madrid, Spain;  Orcidhttps://orcid.org/0000-0001-7156-5939
    • Violeta Vázquez-González - Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
    • Markéta Paloncýová - Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden;  Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 779 00 Olomouc, Czech Republic;  Orcidhttps://orcid.org/0000-0002-6811-7761
    • Irene Sancho-Casado - Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain;  Orcidhttps://orcid.org/0000-0002-3119-4157
    • Fátima Aparicio - Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
    • Alberto de Juan - Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Universidad Autónoma de Madrid, 28049 Madrid, Spain
    • Giovanna Longhi - Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy;  Orcidhttps://orcid.org/0000-0002-0011-5946
    • Patrick Norman - Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden;  Orcidhttps://orcid.org/0000-0002-1191-4954
  • Author Contributions

    All authors have given approval to the final version of the manuscript.

  • Funding

    European Research Council (ERC-Starting Grant 279548 PROGRAM-NANO), MICINN (CTQ2017-84727-P, RED2018-102331-T, and PID2020-116921GB-I00).

  • Notes
    The authors declare no competing financial interest.

Acknowledgments

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Funding from the European Research Council (ERC-Starting Grant 279548 PROGRAM-NANO) MCIN (RED2018-102331-T, PID2020-116921GB-I00, and TED2021-132602B-I00), the Italian Ministry of Education, University and Research (PRIN project prot. 2017A4XRCA_003), the Ministry of Education, Youth, and Sports of the Czech Republic (CZ.02.1.01/0.0/0.0/16_019/0000754, e-INFRA CZ (ID:90254)), the Swedish Research Council (2018-4343), and the Swedish e-Science Research Centre (SeRC) is gratefully acknowledged. The authors also acknowledge the provision of supercomputer resources from the Swedish National Infrastructure for Computing (SNIC). F.A. is grateful to MCIN and Next Generation EU funding for a “Ramon-y-Cajal” fellowship (RyC-2021-031538-I). A.dJ. is grateful to EU funding from a MSCA-IEF action (897507-SuprAlloCat).

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    The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resoln. structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homol. to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomog. anal. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resoln. view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the resp. region in M-PMV. Our results reveal a hollow column of d. for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position.
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  4. 4
    Dutzler, R.; Campbell, E. B.; Cadene, M.; Chait, B. T.; MacKinnon, R. X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity. Nature 2002, 415, 287– 294,  DOI: 10.1038/415287a
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    X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity
    Dutzler, Raimund; Campbell, Ernest B.; Cadene, Martine; Chait, Brian T.; MacKinnon, Roderlelc
    Nature (London, United Kingdom) (2002), 415 (6869), 287-294CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
    The ClC Cl- channels catalyze the selective flow of Cl- ions across cell membranes, thereby regulating elec. excitation in skeletal muscle and the flow of salt and water across epithelial barriers. Genetic defects in ClC Cl- channels underlie several familial muscle and kidney diseases. Here, the authors present the x-ray crystal structures of 2 prokaryotic ClC Cl- channels from Salmonella enterica serovar typhimurium and Escherichia coli at 3.0 and 3.5 Å, resp. Both structures revealed 2 identical pores, each pore being formed by a sep. subunit contained within a homodimeric membrane protein. Individual subunits were composed of 2 roughly repeated halves that spanned the membrane with opposite orientations. This antiparallel architecture defined a selectivity filter in which a Cl- ion was stabilized by electrostatic interactions with α-helix dipoles and by chem. coordination with N atoms and OH groups. These findings provide a structural basis for further understanding the function of ClC Cl- channels, and establish the phys. and chem. basis of their anion selectivity.
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  5. 5
    Shimizu, T. Self-Assembly of Discrete Organic Nanotubes. Bull. Chem. Soc. Jpn. 2018, 91, 623– 668,  DOI: 10.1246/bcsj.20170424
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    Self-assembly of discrete organic nanotubes
    Shimizu, Toshimi
    Bulletin of the Chemical Society of Japan (2018), 91 (4), 623-668CODEN: BCSJA8; ISSN:0009-2673. (Chemical Society of Japan)
    A review. Not only amphiphiles but also non-amphiphilic or π-conjugated mols., if rationally designed, have been found to self-assemble in liq. media to form discrete tubular architectures with well-defined dimensions. This review covers most of the mol. building blocks that spontaneously produce org. nanotubes (ONTs) through self-assembly. Starting with the comparison of synthetic procedures and phys. properties between the ONTs and carbon nanotubes (CNTs), the author discusses the classification of formation mechanism for the self-assembled ONTs. Then, membrane- or sheet-based, nanoring- or nanotoroid-based, stacking-based, and supramol. stacking-based pathways of the self-assembly are described in relation to the presence or absence of intermediate structures. Concerning the membrane- or sheet-based mechanism, the mol. design and functionalities of each building block, and the dimensions of obtained ONTs are discussed in terms of the self-assembling features of amino acids, bile acids, carbohydrates, nucleotides, photoresponsive amphiphiles, functional dyes, fused aroms., carbon allotropes, heterocycles, peptide derivs., and other related mols. Naphthalenediimide, porphyrins, and azobenzene amphiphiles are introduced to feature the ONT formation mediated by nanoring or nanotoroid structures. Cyclic peptides, polymer cyclic peptides, and peptide helixes are then described as building blocks that result in the stacking-based self-assembly of the ONTs. Trimesic acids, pyrimido pyrimidine, ferrocene aroms., and bent-shaped or cyclic arom. amphiphiles are also discussed from the viewpoint of supramol. stacking into the ONTs. Finally, currently important but crit. issues for further development of the ONTs toward practical applications are described.
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  6. 6
    Shimizu, T.; Ding, W.; Kameta, N. Soft-Matter Nanotubes: A Platform for Diverse Functions and Applications. Chem. Rev. 2020, 120, 2347– 2407,  DOI: 10.1021/acs.chemrev.9b00509
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    6
    Soft-Matter Nanotubes: A Platform for Diverse Functions and Applications
    Shimizu, Toshimi; Ding, Wuxiao; Kameta, Naohiro
    Chemical Reviews (Washington, DC, United States) (2020), 120 (4), 2347-2407CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
    A review. Self-assembled org. nanotubes made of single or multiple mol. components can be classified into soft-matter nanotubes (SMNTs) by contrast with hard-matter nanotubes, such as carbon and other inorg. nanotubes. To date, diverse self-assembly processes and elaborate template procedures using rationally designed org. mols. have produced suitable tubular architectures with definite dimensions, structural complexity, and hierarchy for expected functions and applications. Herein, we comprehensively discuss every functions and possible applications of a wide range of SMNTs as bulk materials or single components. This Review highlights valuable contributions mainly in the past decade. Fifteen different families of SMNTs are discussed from the viewpoints of chem., phys., biol., and medical applications, as well as action fields (e.g., interior, wall, exterior, whole structure, and ensemble of nanotubes). Chem. applications of the SMNTs are assocd. with encapsulating materials and sensors. SMNTs also behave, while sometimes undergoing morphol. transformation, as a catalyst, template, liq. crystal, hydro-/organogel, superhydrophobic surface, and micron size engine. Phys. functions pertain to ferro-/piezoelectricity and energy migration/storage, leading to the applications to electrodes or supercapacitors, and mech. reinforcement. Biol. functions involve artificial chaperone, transmembrane transport, nanochannels, and channel reactors. Finally, medical functions range over drug delivery, nonviral gene transfer vector, and virus trap.
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  7. 7
    Shimizu, T.; Masuda, M.; Minamikawa, H. Supramolecular Nanotube Architectures Based on Amphiphilic Molecules. Chem. Rev. 2005, 105, 1401– 1444,  DOI: 10.1021/cr030072j
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    7
    Supramolecular Nanotube Architectures Based on Amphiphilic Molecules
    Shimizu, Toshimi; Masuda, Mitsutoshi; Minamikawa, Hiroyuki
    Chemical Reviews (Washington, DC, United States) (2005), 105 (4), 1401-1443CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
    A review. We here present the principle of chiral self-assembly for the formation of lipid nanotube, its prepn. methods, application possibilities, and novel properties.
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  8. 8
    Chapman, R.; Danial, M.; Koh, M. L.; Jolliffe, K. A.; Perrier, S. Design and properties of functional nanotubes from the self-assembly of cyclic peptide templates. Chem. Soc. Rev. 2012, 41, 6023– 6041,  DOI: 10.1039/c2cs35172b
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    8
    Design and properties of functional nanotubes from the self-assembly of cyclic peptide templates
    Chapman, Robert; Danial, Maarten; Koh, Ming Liang; Jolliffe, Katrina A.; Perrier, Sebastien
    Chemical Society Reviews (2012), 41 (18), 6023-6041CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
    A review. β-Sheet forming self-assembling cyclic peptides offer a versatile scaffold for the construction and control of hydrogen-bonded nanotube assemblies. These structures have major advantages over other nanoscale tubular structures, including sub-nanometer control over the internal diam., and the ability to control internal and external chem. functionality. This tutorial review presents an overview of nanotubes derived from this class of cyclic peptides. The design rationale for functional nanotubes based on cyclic peptide ring size and chem. functionality is discussed. Addnl., the authors highlight the recent expansion of the nanotube toolbox through conjugation of (macro)mols. to the cyclic peptides. These provide addnl. functionality and control nanotube dimensions that could potentially prove beneficial in future applications.
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  9. 9
    Gong, B.; Shao, Z. Self-Assembling Organic Nanotubes with Precisely Defined, Sub-nanometer Pores: Formation and Mass Transport Characteristics. Acc. Chem. Res. 2013, 46, 2856– 2866,  DOI: 10.1021/ar400030e
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    9
    Self-Assembling Organic Nanotubes with Precisely Defined, Sub-nanometer Pores: Formation and Mass Transport Characteristics
    Gong, Bing; Shao, Zhifeng
    Accounts of Chemical Research (2013), 46 (12), 2856-2866CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
    A review. The transport of mols. and ions across nanometer-scaled pores, created by natural or artificial mols., is a phenomenon of both fundamental and practical significance. Biol. channels are the most remarkable examples of mass transport across membranes and demonstrate nearly exclusive selectivity and high efficiency with a diverse collection of mols. These channels are crit. for many basic biol. functions, such as membrane potential, signal transduction, and osmotic homeostasis. If such highly specific and efficient mass transport or sepn. could be achieved with artificial nanostructures under controlled conditions, they could create revolutionary technologies in a variety of areas. For this reason, investigators from diverse disciplines have vigorously studied small non-deformable nanopores. The most exciting studies have focused on carbon nanotubes (CNTs), which have exhibited fast mass transport and high ion selectivity despite their very simple structure. However, the limitations of CNTs and the dearth of other small (≤2 nm) nanopores have severely hampered the systematic investigation of nanopore-mediated mass transport, which will be essential for designing artificial nanopores with desired functions en masse. Researchers can overcome the difficulties assocd. with CNT and other artificial pores by stacking macrocyclic building blocks with persistent shapes to construct tunable, self-assembling org. pores. This effort started when the authors discovered a highly efficient, one-pot macrocyclization process to efficiently prep. several classes of macrocycles with rigid backbones contg. non-deformable cavities. Such macrocycles, if stacked atop one another, should lead to nanotubular assemblies with defined inner pores detd. by their constituent macrocycles. One class of macrocycles with arom. oligoamide backbones had a very high propensity for directional assembly, forming nanotubular structures contg. nanometer and sub-nanometer hydrophilic pores. These self-assembling hydrophilic pores can form ion channels in lipid membranes with very large ion conductances. To control the assembly, the authors have further introduced multiple hydrogen-bonding side chains to enforce the stacking of rigid macrocycles into self-assembling nanotubes. This strategy has produced a self-assembling, sub-nanometer hydrophobic pore that not only acted as a transmembrane channel with surprisingly high ion selectivity, but also mediated a significant transmembrane water flux. The stacking of rigid macrocycles that can be chem. modified in either the lumen or the exterior surface can produce self-assembling org. nanotubes with inner pores of defined sizes. The combination of this approach with the availability and synthetic tunability of various rigid macrocycles should produce a variety of org. nanopores. Such structures would allow researchers to systematically explore mass transport in the sub-nanometer regime. Further advances should lead to novel applications such as biosensing, materials sepn., and mol. purifications.
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  10. 10
    Shimizu, L. S.; Salpage, S. R.; Korous, A. A. Functional Materials from Self-Assembled Bis-urea Macrocycles. Acc. Chem. Res. 2014, 47, 2116– 2127,  DOI: 10.1021/ar500106f
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    10
    Functional Materials from Self-Assembled Bis-urea Macrocycles
    Shimizu, Linda S.; Salpage, Sahan R.; Korous, Arthur A.
    Accounts of Chemical Research (2014), 47 (7), 2116-2127CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
    A review. This Account highlights the work from our labs. on bis-urea macrocycles constructed from two C-shaped spacers and two urea groups. These simple mol. units assembled with high fidelity into columnar structures guided by the three-centered urea hydrogen bonding motif and aryl stacking interactions. Individual columns are aligned and closely packed together to afford functional and homogeneous microporous crystals. This approach allows for precise and rational control over the dimensions of the columnar structure simply by changing the small mol. unit. When the macrocyclic unit lacks a cavity, columnar assembly gives strong pillars. Strong pillars with external functional groups such as basic lone pairs can expand like clays to accept guests between the pillars. Macrocycles that contain sizable interior cavities assemble into porous mol. crystals with aligned, well-defined columnar pores that are accessible to gases and guests. Herein, we examine the optimal design of the macrocyclic unit that leads to columnar assembly in high fidelity and probe the feasibility of incorporating a second functional group within the macrocycles. The porous mol. crystals prepd. through the self-assembly of bis-urea macrocycles display surface areas similar to zeolites but lower than MOFs. Their simple one-dimensional channels are well-suited for studying binding, investigating transport, diffusion and exchange, and monitoring the effects of encapsulation on reaction mechanism and product distribution. Guests that complement the size, shape, and polarity of the channels can be absorbed into these porous crystals with repeatable stoichiometry to form solid host-guest complexes. Heating or extn. with an org. solvent enables desorption or removal of the guest and subsequent recovery of the solid host. Further, these porous crystals can be used as containers for the selective [2 + 2] cycloaddns. of small enones such as 2-cyclohexenone or 3-methyl-cyclopentenone, while larger hosts bind and facilitate the photodimerization of coumarin. When the host framework incorporates benzophenone, a triplet sensitizer, UV-irradn. in the presence of oxygen efficiently generates singlet oxygen. Complexes of this host were employed to influence the selectivity of photooxidns. of 2-methyl-2-butene and cumene with singlet oxygen. Small systematic changes in the channel and bound reactants should enable systematic evaluation of the effects of channel dimensions, guest dimensions, and channel-guest interactions on the processes of absorption, diffusion, and reaction of guests within these nanochannels. Such studies could help in the development of new materials for sepns., gas storage, and catalysis.
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  11. 11
    Fuertes, A.; Juanes, M.; Granja, J. R.; Montenegro, J. Supramolecular functional assemblies: dynamic membrane transporters and peptide nanotubular composites. Chem. Commun. 2017, 53, 7861– 7871,  DOI: 10.1039/C7CC02997G
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    11
    Supramolecular functional assemblies: dynamic membrane transporters and peptide nanotubular composites
    Fuertes, Alberto; Juanes, Marisa; Granja, Juan R.; Montenegro, Javier
    Chemical Communications (Cambridge, United Kingdom) (2017), 53 (56), 7861-7871CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    A review on the recent development in supramol. chem. to help fabricate functional mol. devices, focusing on the prepn. of supramol. membrane transporters with special emphasis on the application of dynamic covalent bonds, and the prepn. of peptide nanotube hybrids with functional applications.
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  12. 12
    Picini, F.; Schneider, S.; Gavat, O.; Vargas Jentzsch, A.; Tan, J.; Maaloum, M.; Strub, J.-M.; Tokunaga, S.; Lehn, J.-M.; Moulin, E.; Giuseppone, N. Supramolecular Polymerization of Triarylamine-Based Macrocycles into Electroactive Nanotubes. J. Am. Chem. Soc. 2021, 143, 6498– 6504,  DOI: 10.1021/jacs.1c00623
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    12
    Supramolecular Polymerization of Triarylamine-Based Macrocycles into Electroactive Nanotubes
    Picini, Flavio; Schneider, Susanne; Gavat, Odile; Vargas Jentzsch, Andreas; Tan, Junjun; Maaloum, Mounir; Strub, Jean-Marc; Tokunaga, Shoichi; Lehn, Jean-Marie; Moulin, Emilie; Giuseppone, Nicolas
    Journal of the American Chemical Society (2021), 143 (17), 6498-6504CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    A S6-sym. triarylamine-based macrocycle (i.e., hexaaza[16]paracyclophane), decorated with six lateral amide functions, is synthesized by a convergent and modular strategy. This macrocycle is shown to undergo supramol. polymn. in o-dichlorobenzene, and its nanotubular structure is elucidated by a combination of spectroscopy and microscopy techniques, together with X-ray scattering and mol. modeling. Upon sequential oxidn., a spectroelectrochem. anal. of the supramol. polymer suggests an extended electronic delocalization of charge carriers both within the macrocycles (through bond) and between the macrocycles along the stacking direction (through space).
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  13. 13
    Bae, K.; Lee, D. G.; Khazi, M. I.; Kim, J. M. Stimuli-Responsive Polydiacetylene Based on the Self-Assembly of a Mercury-Bridged Macrocyclic Diacetylene Dimer. Macromolecules 2022, 55, 2882– 2891,  DOI: 10.1021/acs.macromol.1c02583
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    13
    Stimuli-Responsive Polydiacetylene Based on the Self-Assembly of a Mercury-Bridged Macrocyclic Diacetylene Dimer
    Bae, Kwangmin; Lee, Dong Geol; Khazi, Mohammed Iqbal; Kim, Jong-Man
    Macromolecules (Washington, DC, United States) (2022), 55 (7), 2882-2891CODEN: MAMOBX; ISSN:0024-9297. (American Chemical Society)
    The metal-mediated self-assembly process allows the well-directed and controlled construction of supramol. architectures, and the assembled metal-ligand complexes display diverse functionalities depending on the compn. of the complex template. Through the deliberate introduction of a metal-binding nucleobase, cytosine, to the macrocyclic diacetylene (MCDA), a macrocyclic ligand, CytMCDA, was synthesized. On account of the metal affinity of cytosine and the π-π interaction of the diacetylene template, a Hg-coordinated unidirectional columnar self-assembly of CytMCDA was generated that formed into org. nanotubes. The monomeric CytMCDA-Hg is covalently crosslinked to the blue-phase macrocyclic polydiacetylene nanotubes (CytMCPDA-Hg) via UV-induced topochem. polymn. CytMCPDA-Hg displayed a naked-eye-detectable sensing response toward heat and solvents with a brilliant blue-red chromatic transition. Moreover, owing to the high affinity of the mercury complex toward sulfur, CytMCPDA-Hg displayed a high sensitivity against thiols.
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  14. 14
    Roesner, E. K.; Asheghali, D.; Kirillova, A.; Strauss, M. J.; Evans, A. M.; Becker, M. L.; Dichtel, W. R. Arene–perfluoroarene interactions confer enhanced mechanical properties to synthetic nanotubes. Chem. Sci. 2022, 13, 2475– 2480,  DOI: 10.1039/D1SC05932G
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    14
    Arene-perfluoroarene interactions confer enhanced mechanical properties to synthetic nanotubes
    Roesner, Emily K.; Asheghali, Darya; Kirillova, Alina; Strauss, Michael J.; Evans, Austin M.; Becker, Matthew L.; Dichtel, William R.
    Chemical Science (2022), 13 (8), 2475-2480CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
    Supramol. nanotubes prepd. through macrocycle assembly offer unique properties that stem from their long-range order, structural predictability, and tunable microenvironments. However, assemblies that rely on weak non-covalent interactions often have limited aspect ratios and poor mech. integrity, which diminish their utility. Here pentagonal imine-linked macrocycles are prepd. by condensing a pyridine-contg. diamine and either terephthalaldehyde or 2,3,5,6-tetrafluoroterephthalaldehyde. Atomic force microscopy and synchrotron in solvo X-ray diffraction demonstrate that protonation of the pyridine groups drives assembly into high-aspect ratio nanotube assemblies. A 1 : 1 mixt. of each macrocycle yielded nanotubes with enhanced crystallinity upon protonation. UV-Vis and fluorescence spectroscopy indicate that nanotubes contg. both arene and perfluoroarene subunits display spectroscopic signatures of arene-perfluoroarene interactions. Touch-spun polymeric fibers contg. assembled nanotubes prepd. from the perhydro- or perfluorinated macrocycles exhibited Young's moduli of 1.09 and 0.49 GPa, resp. Fibers contg. nanotube assemblies reinforced by arene-perfluoroarene interactions yielded a 93% increase in the Young's modulus over the perhydro deriv., up to 2.1 GPa. These findings demonstrate that tuning the chem. compn. of the monomeric macrocycles can have profound effects on the mech. strength of the resulting assemblies. More broadly, these results will inspire future studies into tuning orthogonal non-covalent interactions between macrocycles to yield nanotubes with emergent functions and technol. potential.
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  15. 15
    Yashima, E.; Ousaka, N.; Taura, D.; Shimomura, K.; Ikai, T.; Maeda, K. Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions. Chem. Rev. 2016, 116, 13752– 13990,  DOI: 10.1021/acs.chemrev.6b00354
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    15
    Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions
    Yashima, Eiji; Ousaka, Naoki; Taura, Daisuke; Shimomura, Kouhei; Ikai, Tomoyuki; Maeda, Katsuhiro
    Chemical Reviews (Washington, DC, United States) (2016), 116 (22), 13752-13990CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
    A review. In this review, we describe the recent advances in supramol. helical assemblies formed from chiral and achiral small mols., oligomers (foldamers), and helical and nonhelical polymers from the viewpoints of their formations with unique chiral phenomena, such as amplification of chirality during the dynamic helically assembled processes, properties, and specific functionalities, some of which have not been obsd. in or achieved by biol. systems. In addn., a brief historical overview of the helical assemblies of small mols. and remarkable progress in the synthesis of single-stranded and multistranded helical foldamers and polymers, their properties, structures, and functions, mainly since 2009, will also be described.
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    Mayoral, M. J.; Bilbao, N.; González-Rodríguez, D. Hydrogen-Bonded Macrocyclic Supramolecular Systems in Solution and on Surfaces. ChemistryOpen 2016, 5, 10– 32,  DOI: 10.1002/open.201500171
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    16
    Hydrogen-Bonded Macrocyclic Supramolecular Systems in Solution and on Surfaces
    Mayoral, Maria J.; Bilbao, Nerea; Gonzalez-Rodriguez, David
    ChemistryOpen (2016), 5 (1), 10-32CODEN: CHOPCK; ISSN:2191-1363. (Wiley-VCH Verlag GmbH & Co. KGaA)
    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 mol with two binding-sites. Taking advantage of intramol binding events, which are favored with respect to intermol binding in soln., can afford quant amts of a given supramol species under thermodn 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 soln or surface characterization techniques.
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    Aparicio, F.; Mayoral, M. J.; Montoro-García, C.; González-Rodríguez, D. Guidelines for the assembly of hydrogen-bonded macrocycles. Chem. Commun. 2019, 55, 7277– 7299,  DOI: 10.1039/C9CC03166A
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    17
    Guidelines for the assembly of hydrogen-bonded macrocycles
    Aparicio F; Mayoral M J; Montoro-Garcia C; Gonzalez-Rodriguez D
    Chemical communications (Cambridge, England) (2019), 55 (51), 7277-7299 ISSN:.
    The formation of well-defined, discrete self-assembled architectures relies on the interplay between non-covalent interactions and cooperative phenomena. In particular, chelate or intramolecular cooperativity is responsible for the assembly of closed, cyclic structures in competition with open, linear oligomers, and it can be enhanced in several ways to increase the stability of a given cycle size. In this article, we review the work of several researchers on the synthesis of hydrogen-bonded macrocycles from ditopic molecules and analyze the main factors, often interrelated, that influence the equilibrium between ring and chain species. Emphasis will be set on the diverse features that can increase cyclization fidelity, including monomer geometry, template effects, conformational effects, intramolecular interactions and H-bonding pattern.
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    Chamorro, P. B.; Aparicio, F. Chiral nanotubes self-assembled from discrete non-covalent macrocycles. Chem. Commun. 2021, 57, 12712– 12724,  DOI: 10.1039/D1CC04968B
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    18
    Chiral nanotubes self-assembled from discrete non-covalent macrocycles
    Chamorro, P. B.; Aparicio, F.
    Chemical Communications (Cambridge, United Kingdom) (2021), 57 (95), 12712-12724CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    A review. Many strategies have been used to construct supramol. hollow tubes, including helical folding of oligomers, bundling of rod-like structures, rolling-up of sheets and stacking of covalent cycles. On the other hand, controlling chirality at the supramol. level continues attracting much interest because of its implications in future applications of porous systems. This review article covers the main examples in the literature that use simple mol. structures as chiral units for precise assembly into discrete non-covalent cyclic structures that are able to form chiral supramol. tubular systems.
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    Beingessner, R. L.; Fan, Y.; Fenniri, H. Molecular and supramolecular chemistry of rosette nanotubes. RSC Adv. 2016, 6, 75820– 75838,  DOI: 10.1039/C6RA16315G
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    Molecular and supramolecular chemistry of rosette nanotubes
    Beingessner, Rachel L.; Fan, Yiwen; Fenniri, Hicham
    RSC Advances (2016), 6 (79), 75820-75838CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)
    A review. The synthetic strategies, properties and applications of pyrimido[4,5-d]pyrimidine based rosette nanotubes were reviewed. A pyrimido[4,5-d]pyrimidine featuring the hydrogen bond donors and acceptors of both guanine (G) and cytosine (C) in the appropriate geometry was found to undergo hierarchical self-assembly into nanotubular architectures. Specifically, in soln. this heterocycle self-organized into cyclic hexamers through hydrogen bonding interactions, which then further π-π stack into rosette nanotubes (RNTs).
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  20. 20
    Stefan, L.; Monchaud, D. Applications of guanine quartets in nanotechnology and chemical biology. Nat. Rev. Chem. 2019, 3, 650– 668,  DOI: 10.1038/s41570-019-0132-0
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    Yagai, S.; Kitamoto, Y.; Datta, S.; Adhikari, B. Supramolecular Polymers Capable of Controlling Their Topology. Acc. Chem. Res. 2019, 52, 1325– 1335,  DOI: 10.1021/acs.accounts.8b00660
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    Supramolecular Polymers Capable of Controlling Their Topology
    Yagai, Shiki; Kitamoto, Yuichi; Datta, Sougata; Adhikari, Bimalendu
    Accounts of Chemical Research (2019), 52 (5), 1325-1335CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
    One important class of supramol. materials is one-dimensionally elongated supramol. polymers, in which monomers are assocd. by reversible intermol. interactions, yielding a fibrous morphol. Unlike frequently reported conventional supramol. polymers based on, for instance, host-guest interactions, those composed of one-dimensionally stacked π-conjugated mols. can be encoded with high degrees of internal order by cooperative assocn. of the rigid arom. monomers, endowing such supramol. polymers with extraordinary properties and functionality. However, their internal order has not yet been exploited to manipulate the complex landscape of well-defined states of the supramol. polymer backbone, which may induce new functionalities beyond the intrinsic properties of the backbones.This Account will focus on the inceptive phase of our research on supramol. polymers with high degrees of internal order able to impart intrinsic curvature to their backbones. Initially, we developed a naphthalene mol. functionalized with barbituric acid, which forms uniform toroidal short fibers with diams. of approx. 16 nm via the formation of hydrogen-bonded cyclic hexamers (rosettes). As we thought the uniformity of the toroid size to arise from the intrinsic curvature generated upon stacking of the rosettes, we exploited this intrinsic curvature to design continuously curved extended supramol. polymers by extension of such mol. π-systems. The intrinsic curvature produced by the monomers with more expanded π-systems indeed gave us access to higher-order structures (topologies) ranging from randomly folded to helically folded coils in extended supramol. polymers. We will discuss the kinetic aspects of the generation of intrinsic curvature for topol. control, including the formation of toroidal structures resulting from ring-closing processes.For extended supramol. polymers with well-defined topologies, we will discuss manipulation of a complex landscape of well-defined states by external stimuli. The incorporation of a photoresponsive azobenzene chromophore in the original naphthalene mol. scaffold allowed us to reversibly destroy or recover the curvature of the main chain through trans-cis photoisomerization. By means of this photocontrollable curvature, we have demonstrated light-induced unfolding of helically folded structures into entirely stretched structures. Furthermore, a direct extension of the π-conjugated core provided us with access to unprecedented supramol. polymers with emergent time-dependent topol. transitions. Mols. with a naphthalene core conjugated with two phenylene units kinetically afforded supramol. polymers that consist of helically folded and misfolded domains. Upon aging the supramol. polymer soln., we obsd. spontaneous folding of the misfolded domains in a time scale of days, eventually obtaining a supramol. polymer topol. analogous to the tertiary structure of proteins. These supramol. polymers with unrivaled and active topologies provide new prospects for supramol. polymers as one-dimensional nanomaterials.
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  22. 22
    Jonkheijm, P.; Miura, A.; Zdanowska, M.; Hoeben, F. J. M.; De Feyter, S.; Schenning, A. P. H. J.; De Schryver, F. C.; Meijer, E. W. π-Conjugated Oligo-(p-phenylenevinylene) Rosettes and Their Tubular Self-Assembly. Angew. Chem., Int. Ed. 2004, 43, 74– 78,  DOI: 10.1002/anie.200352790
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    π-Conjugated oligo(p-phenylenevinylene) rosettes and their tubular self-assembly
    Jonkheijm, Pascal; Miura, Atsushi; Zdanowska, Magdalena; Hoeben, Freek J. M.; De Feyter, Steven; Schenning, Albertus P. H. J.; De Schryver, Frans C.; Meijer, E. W.
    Angewandte Chemie, International Edition (2004), 43 (1), 74-78CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Oligo(p-phenylenevinylene)s with pendant diaminotriazine moieties can self-assemble through hydrogen-bonding interactions to give hexameric rosettes. These rosettes further organize into large supramol. tubes with perfect space filling.
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  23. 23
    Schuster, G. B.; Cafferty, B. J.; Karunakaran, S. C.; Hud, N. V. Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA. J. Am. Chem. Soc. 2021, 143, 9279– 9296,  DOI: 10.1021/jacs.0c13081
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    23
    Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA
    Schuster, Gary B.; Cafferty, Brian J.; Karunakaran, Suneesh C.; Hud, Nicholas V.
    Journal of the American Chemical Society (2021), 143 (25), 9279-9296CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    A review. The hypothesis that RNA and DNA are products of chem. and biol. evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramol. polymers. These structures exhibit properties that provide robust solns. to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examn. by exptl. and computational methods provides insight into the chem. and phys. principles that govern a particular class of water-sol. one-dimensional supramol. polymers. In addn. to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of pos. charged, planar compds.; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent crosslinking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramol. structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-sol. supramol. polymers.
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  24. 24
    Tripathi, P.; Shuai, L.; Joshi, H.; Yamazaki, H.; Fowle, W. H.; Aksimentiev, A.; Fenniri, H.; Wanunu, M. Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors. J. Am. Chem. Soc. 2020, 142, 1680– 1685,  DOI: 10.1021/jacs.9b10993
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    24
    Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors
    Tripathi, Prabhat; Shuai, Liang; Joshi, Himanshu; Yamazaki, Hirohito; Fowle, William H.; Aksimentiev, Aleksei; Fenniri, Hicham; Wanunu, Meni
    Journal of the American Chemical Society (2020), 142 (4), 1680-1685CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Rosette nanotubes (RNTs) are a class of materials formed by mol. self-assembly of a fused guanine-cytosine base (G C base). An important feature of these self-assembled nanotubes is their precise at. structure, intriguing for rational design and optimization as synthetic transmembrane porins. Here, we present exptl. observations of ion transport across 1.1 nm inner diam. RNT porins (RNTPs) of various lengths in the range 5-200 nm. In a typical expt., custom lipophilic RNTPs were first inserted into lipid vesicles; the vesicles then spontaneously fused with a planar lipid bilayer, which produced stepwise increases of ion current across the bilayer. Our measurements in 1 M KCl soln. indicate ion transport rates of ∼50 ions s-1 V-1 m, which for short channels amts. to conductance values of ∼1 nS, commensurate with naturally occurring toxin channels such as α-hemolysin. Measurements of interaction times of α-cyclodextrin with RNTPs reveal two distinct unbinding time scales, which suggest that interactions of either face of α-cyclodextrin with the RNTP face are differentiable, backed with all-atom mol. dynamics simulations. Our results highlight the potential of RNTPs as self-assembled nonproteinaceous single-mol. sensors and selective nanofilters with tunable functionality through chem.
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    Fukino, T.; Joo, H.; Hisada, Y.; Obana, M.; Yamagishi, H.; Hikima, T.; Takata, M.; Fujita, N.; Aida, T. Manipulation of Discrete Nanostructures by Selective Modulation of Noncovalent Forces. Science 2014, 344, 499– 504,  DOI: 10.1126/science.1252120
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    Manipulation of Discrete Nanostructures by Selective Modulation of Noncovalent Forces
    Fukino, Takahiro; Joo, Hyunho; Hisada, Yuki; Obana, Maiko; Yamagishi, Hiroshi; Hikima, Takaaki; Takata, Masaki; Fujita, Norifumi; Aida, Takuzo
    Science (Washington, DC, United States) (2014), 344 (6183), 499-504CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    Ferrocene-based tetratopic pyridyl ligands, that can dynamically change their geometry by means of thermal rotation of their cyclopentadienyl rings in soln., has been obsd. to assemble with AgBF4 into discrete metal-org. nanotubes with large and uniform diams. The nanotubes could be cut into metal-org. nanorings through selective attenuation of the inter-nanoring interaction via ferrocene oxidn. The resultant nanorings could be transferred onto inorg. substrates electrostatically or allowed to reassemble to form the original nanotube by the reductive neutralization of their oxidized ferrocene units.
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    Huang, Z.; Kang, S.-K.; Banno, M.; Yamaguchi, T.; Lee, D.; Seok, C.; Yashima, E.; Lee, M. Pulsating Tubules from Noncovalent Macrocycles. Science 2012, 337, 1521– 1526,  DOI: 10.1126/science.1224741
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    Pulsating Tubules from Noncovalent Macrocycles
    Huang, Zhegang; Kang, Seong-Kyun; Banno, Motonori; Yamaguchi, Tomoko; Lee, Dongseon; Seok, Chaok; Yashima, Eiji; Lee, Myongsoo
    Science (Washington, DC, United States) (2012), 337 (6101), 1521-1526CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    Despite recent advances in synthetic nanometer-scale tubular assembly, conferral of dynamic response characteristics to the tubules remains a challenge. Here, we report on supramol. nanotubules that undergo a reversible contraction-expansion motion accompanied by an inversion of helical chirality. Bent-shaped arom. amphiphiles self-assemble into hexameric macrocycles in aq. soln., forming chiral tubules by spontaneous one-dimensional stacking with a mutual rotation in the same direction. The adjacent arom. segments within the hexameric macrocycles reversibly slide along one another in response to external triggers, resulting in pulsating motions of the tubules accompanied by a chiral inversion. The arom. interior of the self-assembled tubules encapsulates hydrophobic guests such as carbon-60 (C60). Using a thermal trigger, we could regulate the C60-C60 interactions through the pulsating motion of the tubules.
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    Tashiro, K.; Saito, T.; Arima, H.; Suda, N.; Vedhanarayanan, B.; Yagai, S. Scissor-Shaped Photochromic Dyads: Hierarchical Self-Assembly and Photoresponsive Property. Chem. Rec. 2022, 22, e202100252  DOI: 10.1002/tcr.202100252
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    27
    Scissor-Shaped Photochromic Dyads: Hierarchical Self-Assembly and Photoresponsive Property
    Tashiro, Keigo; Saito, Takuho; Arima, Hironari; Suda, Natsuki; Vedhanarayanan, Balaraman; Yagai, Shiki
    Chemical Record (2022), 22 (2), e202100252CODEN: CRHEAK; ISSN:1528-0691. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Unique relationships between hierarchically organized biol. nanostructures and functions have motivated chemists to construct sophisticated artificial nanostructured systems from small and simple synthetic mols. through self assembly. As one of such sophisticated systems, we have investigated scissor shaped photochromic dyads that can hierarchically self assemble into discrete nanostructures showing photoresponsive properties. We synthesized various azobenzene dyads and found that these dyads adopt intramolecularly folded conformation like a closed scissor, and then self assemble into toroidal nanostructures by generating curvature. The toroids further organize into nanotubes and further into helical supramol. fibers depending on the nature of alkyl substituents. All of these nanostructures can be dissocd. and reorganized through the photoisomerization of azobenzene units. On the other hand, the introduction of stilbene chromophores instead of azobenzenes leads to one-dimensional supramol. polymn., which upon the intramol. photocyclization of stilbene chromophores shifts to curved self assembly leading to helicoidal fibers with distinct supramol. chirality.
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  28. 28
    Shi, Q.; Javorskis, T.; Bergquist, K.-E.; Ulčinas, A.; Niaura, G.; Matulaitienė, I.; Orentas, E.; Wärnmark, K. Stimuli-controlled self-assembly of diverse tubular aggregates from one single small monomer. Nat. Commun. 2017, 8, 14943  DOI: 10.1038/ncomms14943
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    Stimuli-controlled self-assembly of diverse tubular aggregates from one single small monomer
    Shi, Qixun; Javorskis, Tomas; Bergquist, Karl-Erik; Ulcinas, Arturas; Niaura, Gediminas; Matulaitiene, Ieva; Orentas, Edvinas; Waernmark, Kenneth
    Nature Communications (2017), 8 (), 14943pp.CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
    The design and synthesis of new stimuli-responsive hydrogen-bonding monomers that display a diversity of self-assembly pathways is of central importance in supramol. chem. Here we describe the aggregation properties of a simple, intrinsically C2-sym. enantiopure bicyclic cavity compd. bearing a terminally unsubstituted ureidopyrimidinone fragment fused with a pyrrole moiety in different solvents and in the absence and presence of C60 and C70 guests. The tetrameric cyclic aggregate is selectively obtained in chlorinated solvents, where only part of the available hydrogen bonding sites are utilized, whereas in toluene or upon addn. of C70 guests, further aggregation into tubular supramol. polymers is achieved. The open-end cyclic assemblies rearrange into a closed-shell capsule upon introduction of C60 with an accompanied symmetry breaking of the monomer. Our study demonstrates that a C60 switch can be used to simultaneously control the topol. and occupancy of tubular assemblies resulting from the aggregation of small monomers.
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    Liu, C.-Z.; Yan, M.; Wang, H.; Zhang, D.-W.; Li, Z.-T. Making Molecular and Macromolecular Helical Tubes: Covalent and Noncovalent Approaches. ACS Omega 2018, 3, 5165– 5176,  DOI: 10.1021/acsomega.8b00681
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    29
    Making Molecular and Macromolecular Helical Tubes: Covalent and Noncovalent Approaches
    Liu, Chuan-Zhi; Yan, Meng; Wang, Hui; Zhang, Dan-Wei; Li, Zhan-Ting
    ACS Omega (2018), 3 (5), 5165-5176CODEN: ACSODF; ISSN:2470-1343. (American Chemical Society)
    Areview. Arom. foldamers possess well-defined cavity that can be stabilized by discrete intramol. interactions including hydrogen bonding, solvophobicity, electrostatic repulsion, or coordination. Long foldamers can form dynamic deep helical tubular architectures that are not only structurally attractive but also useful hosts for guest encapsulation, chirality induction, delivery, and catalysis. This kind of helical tubular structures can be formed by single mols. or macromols. or by connecting short-folded or helical segments through noncovalent or covalent forces. This perspective summarizes the recent advances on the construction of helical tubes and their properties and functions.
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    Balbo Block, M. A.; Kaiser, C.; Khan, A.; Hecht, S. Discrete Organic Nanotubes Based on a Combination of Covalent and Non-Covalent Approaches. In Functional Molecular Nanostructures; Schlüter, A. D., Ed.; Springer Berlin Heidelberg: Berlin, Heidelberg, 2005; pp 89– 150.
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    Vázquez-González, V.; Mayoral, M. J.; Chamorro, R.; Hendrix, M. M. R. M.; Voets, I. K.; González-Rodríguez, D. Noncovalent Synthesis of Self-Assembled Nanotubes through Decoupled Hierarchical Cooperative Processes. J. Am. Chem. Soc. 2019, 141, 16432– 16438,  DOI: 10.1021/jacs.9b07868
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    31
    Noncovalent Synthesis of Self-Assembled Nanotubes through Decoupled Hierarchical Cooperative Processes
    Vazquez-Gonzalez, Violeta; Mayoral, Maria J.; Chamorro, Raquel; Hendrix, Marco M. R. M.; Voets, Ilja K.; Gonzalez-Rodriguez, David
    Journal of the American Chemical Society (2019), 141 (41), 16432-16438CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Because of their wide no. of biol. functions and potential applications, self-assembled nanotubes constitute highly relevant targets in noncovalent synthesis. Herein, we introduce a novel approach to produce supramol. nanotubes with defined inner and outer diams. 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 polymn.
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    Vázquez-González, V.; Mayoral, M. J.; Aparicio, F.; Martinez-Arjona, P.; Gonzalez-Rodriguez, D. The Role of Peripheral Amide Groups as Hydrogen-Bonding Directors in the Tubular Self-Assembly of Dinucleobase Monomers. ChemPlusChem 2021, 86, 1087– 1096,  DOI: 10.1002/cplu.202100255
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    32
    The Role of Peripheral Amide Groups as Hydrogen-Bonding Directors in the Tubular Self-Assembly of Dinucleobase Monomers
    Vazquez-Gonzalez, Violeta; Mayoral, Maria J.; Aparicio, Fatima; Martinez-Arjona, Paula; Gonzalez-Rodriguez, David
    ChemPlusChem (2021), 86 (8), 1087-1096CODEN: CHEMM5; ISSN:2192-6506. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Nanotubes are a fascinating kind of self-assembled structure which have a wide interest and potential in supramol. chem. We demonstrated that nanotubes of defined dimensions can be produced from dinucleobase monomers through two decoupled hierarchical cooperative processes: cyclotetramerization and supramol. polymn. 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 1H NMR and CD spectroscopy techniques allowed us to analyze quant. the thermodn. of each of these two processes sep. We found out that the presence of these amide directors is essential to guide the polymn. event and that their nature and no. have a strong influence, not only on the stabilization of the stacks of macrocycles, but also on the supramol. polymn. mechanism.
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    Aparicio, F.; Chamorro, P. B.; Chamorro, R.; Casado, S.; González-Rodríguez, D. Nanostructured Micelle Nanotubes Self-Assembled from Dinucleobase Monomers in Water. Angew. Chem., Int. Ed. 2020, 59, 17091– 17096,  DOI: 10.1002/anie.202006877
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    Nanostructured Micelle Nanotubes Self-Assembled from Dinucleobase Monomers in Water
    Aparicio, Fatima; Chamorro, Paula B.; Chamorro, Raquel; Casado, Santiago; Gonzalez-Rodriguez, David
    Angewandte Chemie, International Edition (2020), 59 (39), 17091-17096CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Despite the central importance of aq. amphiphile assemblies in science and industry, the size and shape of these nano-objects is often difficult to control with accuracy owing to the non-directional nature of the hydrophobic interactions that sustain them. Here, using a bioinspired strategy that consists of programming an amphiphile with shielded directional Watson-Crick hydrogen-bonding functions, its self-assembly in water was guided toward a novel family of chiral micelle nanotubes with partially filled lipophilic pores of about 2 nm in diam. Moreover, these tailored nanotubes are successfully demonstrated to ext. and host mols. that are complementary in size and chem. affinity.
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    Chamorro, P. B.; Aparicio, F.; Chamorro, R.; Bilbao, N.; Casado, S.; González-Rodríguez, D. Exploring the tubular self-assembly landscape of dinucleobase amphiphiles in water. Org. Chem. Front. 2021, 8, 686– 696,  DOI: 10.1039/D0QO01110J
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    34
    Exploring the tubular self-assembly landscape of dinucleobase amphiphiles in water
    Chamorro, Paula B.; Aparicio, Fatima; Chamorro, Raquel; Bilbao, Nerea; Casado, Santiago; Gonzalez-Rodriguez, David
    Organic Chemistry Frontiers (2021), 8 (4), 686-696CODEN: OCFRA8; ISSN:2052-4129. (Royal Society of Chemistry)
    The design and prodn. of the next generations of synthetic aq. self-assembled systems able to mimic some biol. features will require increasingly sophisticated monomer constituents that make use of addnl. interactions to hydrophibic effects to attain enhanced structural and functional complexity. Here, we broadly investigate the aq. self-assembly of dinucleobase amphiphilic monomers into helical nanotubes under a wide range of different conditions of temp., concn., solvent compn. and pH. Such monomers comprise an amphiphilic π-conjugated central block, endowed with a lipophilic chiral tail and a hydrophilic group that can be made anionic (carboxylate), neutral (glycol) or cationic (ammonium), disubstituted with complementary guanine and cytosine nucleobases at each termini. These mols. self-assemble into amphiphilic nanotubes in water but, when subjected to diverse (drastic) changes in the exptl. conditions, undergo either disassembly into monomers, chiral reorganization, or a morphol. restructuration into globular objects due to dehydration of the peripheral hydrophilic groups.
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  35. 35
    Montoro-García, C.; Camacho-García, J.; López-Pérez, A. M.; Bilbao, N.; Romero-Pérez, S.; Mayoral, M. J.; González-Rodríguez, D. High-Fidelity Noncovalent Synthesis of Hydrogen-Bonded Macrocyclic Assemblies. Angew. Chem., Int. Ed. 2015, 54, 6780– 6784,  DOI: 10.1002/anie.201501321
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    High-Fidelity Noncovalent Synthesis of Hydrogen-Bonded Macrocyclic Assemblies
    Montoro-Garcia, Carlos; Camacho-Garcia, Jorge; Lopez-Perez, Ana M.; Bilbao, Nerea; Romero-Perez, Sonia; Mayoral, Maria J.; Gonzalez-Rodriguez, David
    Angewandte Chemie, International Edition (2015), 54 (23), 6780-6784CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    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 thermodn. and kinetic stability and is formed with high fidelities within a broad concn. range.
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    Montoro-García, C.; Camacho-García, J.; López-Pérez, A. M.; Mayoral, M. J.; Bilbao, N.; González-Rodríguez, D. Role of the Symmetry of Multipoint Hydrogen Bonding on Chelate Cooperativity in Supramolecular Macrocyclization Processes. Angew. Chem., Int. Ed. 2016, 55, 223– 227,  DOI: 10.1002/anie.201508854
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    Role of the Symmetry of Multipoint Hydrogen Bonding on Chelate Cooperativity in Supramolecular Macrocyclization Processes
    Montoro-Garcia, Carlos; Camacho-Garcia, Jorge; Lopez-Perez, Ana M.; Mayoral, Maria J.; Bilbao, Nerea; Gonzalez-Rodriguez, David
    Angewandte Chemie, International Edition (2016), 55 (1), 223-227CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Herein, the authors analyze the intrinsic chelate effect that multipoint H-bonding patterns exert on the overall energy of dinucleoside cyclic systems. 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 unsym. ADD-DAA or DDA-AAD patterns to the sym. DAD-ADA pattern.
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    Jorgensen, W. L.; Pranata, J. Importance of secondary interactions in triply hydrogen bonded complexes: guanine-cytosine vs uracil-2,6-diaminopyridine. J. Am. Chem. Soc. 1990, 112, 2008– 2010,  DOI: 10.1021/ja00161a061
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    Importance of secondary interactions in triply hydrogen bonded complexes: guanine-cytosine vs uracil-2,6-diaminopyridine
    Jorgensen, William L.; Pranata, Julianto
    Journal of the American Chemical Society (1990), 112 (5), 2008-10CODEN: JACSAT; ISSN:0002-7863.
    Although complexes of guanine-cytosine and uracil-2,6-diaminopyridine are both triply H-bonded in CHCl3, measured assocn. consts. for such systems vary by 102-103. The origin of the discrepancy is analyzed here through computational studies. Monte Carlo statistical mechanics simulations for the complexes in CHCl3 also find the substantial binding preference for guanine-cytosine. The difference is then traced to the gas-phase interaction energies which favor guanine-cytosine complexation by ca. 10 kcal/mol. The three H bonds are of the same type in both complexes; however, the variation in their arrangement leads to secondary electrostatic effects that account for the destabilization of the uracil-2,6-diaminopyridine complex. Such secondary interactions are a significant element for consideration in mol. design.
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    Camacho-García, J.; Montoro-García, C.; López-Perez, A. M.; Bilbao, N.; Romero-Pérez, S.; González-Rodríguez, D. Synthesis and complementary self-association of novel lipophilic [small pi]-conjugated nucleoside oligomers. Org. Biomol. Chem. 2015, 13, 4506– 4513,  DOI: 10.1039/C5OB00098J
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    Synthesis and complementary self-association of novel lipophilic π-conjugated nucleoside oligomers
    Camacho-Garcia, J.; Montoro-Garcia, C.; Lopez-Perez, A. M.; Bilbao, N.; Romero-Perez, S.; Gonzalez-Rodriguez, D.
    Organic & Biomolecular Chemistry (2015), 13 (15), 4506-4513CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)
    A series of lipophilic nucleosides comprising natural and non-natural bases that are π-conjugated to a short oligo-phenylene-ethynylene fragment has been synthesized. These bases comprise guanosine, isoguanosine, and 2-amino-adenosine as purine heterocycles, and cytidine, iso-cytosine and uridine as complementary pyrimidine bases. The hydrogen-bonding dimerization and assocn. processes between complementary bases were also studied by 1H NMR and absorption spectroscopy in order to obtain the relevant assocn. consts.
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    Mayoral, M. J.; Camacho-Garcia, J.; Magdalena-Estirado, E.; Blanco-Lomas, M.; Fadaei, E.; Montoro-Garcia, C.; Serrano-Molina, D.; Gonzalez-Rodriguez, D. Dye-conjugated complementary lipophilic nucleosides as useful probes to study association processes by fluorescence resonance energy transfer. Org. Biomol. Chem. 2017, 15, 7558– 7565,  DOI: 10.1039/C7OB01930K
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    Dye-conjugated complementary lipophilic nucleosides as useful probes to study association processes by fluorescence resonance energy transfer
    Mayoral, M. J.; Camacho-Garcia, J.; Magdalena-Estirado, E.; Blanco-Lomas, M.; Fadaei, E.; Montoro-Garcia, C.; Serrano-Molina, D.; Gonzalez-Rodriguez, D.
    Organic & Biomolecular Chemistry (2017), 15 (36), 7558-7565CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)
    Modern supramol. chem. relies on the combination of diverse anal. techniques that can provide complementary information on complex self-assembly landscapes. Among them, resonance energy transfer, monitored by fluorescence emission spectroscopy, arises as a sensitive and convenient phenomenon to report binding intermol. interactions. The use of mol. probes labeled with suitable complementary energy-transfer pairs can provide valuable information about the thermodn., kinetics and self-sorting characteristics of a particular self-assembled system. The objective of this work is to generate a set of nucleoside FRET probes that can be reliably employed to prove and analyze quant. H-bonding interactions between complementary Watson-Crick pairs. We first describe the prepn. of a set of lipophilic nucleosides that are linked to a π-conjugated functional fragment. The bases include guanosine and 2-aminoadenosine as purine heterocycles, and cytidine and uridine as complementary pyrimidine bases. The π-conjugated moiety comprises either a short phenylene-ethynylene oligomer, a bithiophene, or a BODIPY dye. We then demonstrate that the last two chromophores constitute an energy donor-acceptor couple and that donor emission quenching can be related to the ratio of mols. bound to the complementary acceptor pair. Hence, fluorescence spectroscopy in combination with resonance energy transfer, is shown here to be a useful tool to study and quantify the assocn. and self-sorting events between complementary and non-complementary nucleosides in apolar arom. solvents, where the binding strength is considerably high, and sensitive techniques that employ low concns. are demanded.
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    Serrano-Molina, D.; de Juan, A.; González-Rodríguez, D. Dinucleoside-Based Macrocycles Displaying Unusually Large Chelate Cooperativities. Chem. Rec. 2021, 21, 480– 497,  DOI: 10.1002/tcr.202000141
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    Dinucleoside-based Macrocycles Displaying Unusually Large Chelate Cooperativities
    Serrano-Molina, David; de Juan, Alberto; Gonzalez-Rodriguez, David
    Chemical Record (2021), 21 (3), 480-497CODEN: CRHEAK; ISSN:1528-0691. (Wiley-VCH Verlag GmbH & Co. KGaA)
    A review. High-fidelity prodn. of a single self-assembled species in competition with others relies on achieving strong chelate cooperativities, which can be quantified by the effective molarity parameter. Therefore, supramol. systems displaying very high effective molarities are reliably formed in a wide range of exptl. conditions and exhibit "all-or-none" phenomena, meaning that the assembly is either fully formed or fully dissocd. into the corresponding monomeric components. We summarize here our efforts in the study and characterization of one of these synthetic systems exhibiting record chelate cooperativities: the self-assembly of rod-like dinucleoside mols. into tetrameric macrocycles through hydrogen-bonding Watson-Crick interactions.
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    Romero-Pérez, S.; Camacho-García, J.; Montoro-García, C.; López-Pérez, A. M.; Sanz, A.; Mayoral, M. J.; González-Rodríguez, D. G-Arylated Hydrogen-Bonded Cyclic Tetramer Assemblies with Remarkable Thermodynamic and Kinetic Stability. Org. Lett. 2015, 17, 2664– 2667,  DOI: 10.1021/acs.orglett.5b01042
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    G-Arylated Hydrogen-Bonded Cyclic Tetramer Assemblies with Remarkable Thermodynamic and Kinetic Stability
    Romero-Perez, Sonia; Camacho-Garcia, Jorge; Montoro-Garcia, Carlos; Lopez-Perez, Ana M.; Sanz, Alfredo; Mayoral, Maria Jose; Gonzalez-Rodriguez, David
    Organic Letters (2015), 17 (11), 2664-2667CODEN: ORLEF7; ISSN:1523-7052. (American Chemical Society)
    The prepn. and self-assembly of novel G-C dinucleoside monomers that are equipped with electron-poor aryl groups at the G-N2 amino group have been studied. Such monomers assoc. via Watson-Crick H-bonding into discrete unstrained tetrameric macrocycles that arise as a thermodynamically and kinetically stabilized product in a wide variety of exptl. conditions, including very polar solvent environments and low concns. G-arylation produces an increased stability of the cyclic assembly, as a result of a subtle interplay between enthalpic and entropic effects involving the solvent coordination sphere.
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    Montoro-García, C.; Mayoral, M. J.; Chamorro, R.; González-Rodríguez, D. How Large Can We Build a Cyclic Assembly? Impact of Ring Size on Chelate Cooperativity in Noncovalent Macrocyclizations. Angew. Chem., Int. Ed. 2017, 56, 15649– 15653,  DOI: 10.1002/anie.201709563
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    How Large Can We Build a Cyclic Assembly? Impact of Ring Size on Chelate Cooperativity in Noncovalent Macrocyclizations
    Montoro-Garcia, Carlos; Mayoral, Maria J.; Chamorro, Raquel; Gonzalez-Rodriguez, David
    Angewandte Chemie, International Edition (2017), 56 (49), 15649-15653CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Self-assembled systems rely on intramol. 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 assoc. in cyclic tetramers by complementary Watson-Crick H-bonding interactions. As the monomer length increases, and thus the no. of C(sp)-C(sp2) σ-bonds in the π-conjugated skeleton, the macrocycle stability decreases due to a notable redn. in effective molarity (EM), which has a clear entropic origin. We detd. the relationship between EM or ΔS and the no. of σ-bonds, which allowed us to predict the max. monomer lengths at which cyclic species would still assemble quant., or whether the cyclic species would not able to compete at all with linear oligomers over the whole concn. range.
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    Montoro-García, C.; Bilbao, N.; Tsagri, I. M.; Zaccaria, F.; Mayoral, M. J.; Fonseca Guerra, C.; González-Rodríguez, D. Impact of Conformational Effects on the Ring–Chain Equilibrium of Hydrogen-Bonded Dinucleosides. Chem.–Eur. J. 2018, 24, 11983– 11991,  DOI: 10.1002/chem.201801704
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    Impact of Conformational Effects on the Ring-Chain Equilibrium of Hydrogen-Bonded Dinucleosides
    Montoro-Garcia, Carlos; Bilbao, Nerea; Tsagri, Iris M.; Zaccaria, Francesco; Mayoral, Maria J.; Fonseca Guerra, Celia; Gonzalez-Rodriguez, David
    Chemistry - A European Journal (2018), 24 (46), 11983-11991CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Supramol. ring-vs.-chain equil. are ubiquitous in biol. 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 mol. 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 equil., such as steric hindrance, intramol. interactions, or π-conjugation pathways.
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    Mayoral, M. J.; Serrano-Molina, D.; Camacho-García, J.; Magdalena-Estirado, E.; Blanco-Lomas, M.; Fadaei, E.; González-Rodríguez, D. Understanding complex supramolecular landscapes: non-covalent macrocyclization equilibria examined by fluorescence resonance energy transfer. Chem. Sci. 2018, 9, 7809– 7821,  DOI: 10.1039/C8SC03229G
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    Understanding complex supramolecular landscapes: non-covalent macrocyclization equilibria examined by fluorescence resonance energy transfer
    Mayoral, Maria J.; Serrano-Molina, David; Camacho-Garcia, Jorge; Magdalena-Estirado, Eva; Blanco-Lomas, Marina; Fadaei, Elham; Gonzalez-Rodriguez, David
    Chemical Science (2018), 9 (40), 7809-7821CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
    As mol. self-assembled systems increase in complexity, due to a large no. of participating entities and/or the establishment of multiple competing equil., their full understanding becomes likewise more complicated, and the use of diverse anal. 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 thermodn. data about complex supramol. 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 intermol. assocn. processes of Watson-Crick H-bonding pairs. Multiwavelength anal. of the monomer emission changes allowed us to det. cyclotetramerization consts. 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 expts., fluorescence and CD spectroscopy measurements in different regions of the visible spectrum addnl. reveal intermol. 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.
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    Serrano-Molina, D.; Montoro-García, C.; Mayoral, M. J.; de Juan, A.; González-Rodríguez, D. Self-Sorting Governed by Chelate Cooperativity. J. Am. Chem. Soc. 2022, 144, 5450– 5460,  DOI: 10.1021/jacs.1c13295
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    Self-Sorting Governed by Chelate Cooperativity
    Serrano-Molina, David; Montoro-Garcia, Carlos; Mayoral, Maria J.; de Juan, Alberto; Gonzalez-Rodriguez, David
    Journal of the American Chemical Society (2022), 144 (12), 5450-5460CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Self-sorting phenomena are the basis of manifold relevant (bio)chem. processes where a set of mols. is able to interact with no interference from other sets and are ruled by a no. of codes that are programmed in mol. structures. In this work, we study, the relevance of chelate cooperativity as a code for achieving high self-sorting fidelity. In particular, we establish qual. and quant. relationships between the cooperativity of a cyclic system and the self-sorting fidelity when combined with other mols. that share identical geometry and/or binding interactions. We demonstrate that only systems displaying sufficiently strong chelate cooperativity can achieve quant. narcissistic self-sorting fidelities either by dictating the distribution of cyclic species in complex mixts. or by ruling the competition between the intra- and intermol. versions of a noncovalent interaction.
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    Bilbao, N.; Destoop, I.; De Feyter, S.; González-Rodríguez, D. Two-Dimensional Nanoporous Networks Formed by Liquid-to-Solid Transfer of Hydrogen-Bonded Macrocycles Built from DNA Bases. Angew. Chem., Int. Ed. 2016, 55, 659– 663,  DOI: 10.1002/anie.201509233
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    Two-Dimensional Nanoporous Networks Formed by Liquid-to-Solid Transfer of Hydrogen-Bonded Macrocycles Built from DNA Bases
    Bilbao, Nerea; Destoop, Iris; De Feyter, Steven; Gonzalez-Rodriguez, David
    Angewandte Chemie, International Edition (2016), 55 (2), 659-663CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    We present an approach that makes use of DNA base pairing to produce hydrogen-bonded macrocycles whose supramol. structure can be transferred from soln. to a solid substrate. A hierarchical assembly process ultimately leads to two-dimensional nanostructured porous networks that are able to host size-complementary guests.
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    Chamorro, R.; de Juan-Fernández, L.; Nieto-Ortega, B.; Mayoral, M. J.; Casado, S.; Ruiz-González, L.; Pérez, E. M.; González-Rodríguez, D. Reversible dispersion and release of carbon nanotubes via cooperative clamping interactions with hydrogen-bonded nanorings. Chem. Sci. 2018, 9, 4176– 4184,  DOI: 10.1039/C8SC00843D
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    Reversible dispersion and release of carbon nanotubes via cooperative clamping interactions with hydrogen-bonded nanorings
    Chamorro, Raquel; de Juan-Fernandez, Leire; Nieto-Ortega, Belen; Mayoral, Maria J.; Casado, Santiago; Ruiz-Gonzalez, Luisa; Perez, Emilio M.; Gonzalez-Rodriguez, David
    Chemical Science (2018), 9 (17), 4176-4184CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
    Due to their outstanding electronic and mech. properties, single-walled carbon nanotubes (SWCNTs) are promising nanomaterials for the future generation of optoelectronic devices and composites. However, their scarce soly. limits their application in many technologies that demand soln.-processing of high-purity SWCNT samples. Although some non-covalent functionalization approaches have demonstrated their utility in extg. 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 assoc. intimately with SWCNTs by embracing the tube sidewalls, which allows for an efficient SWCNT debundling and for the prodn. of long-lasting SWCNT dispersions of high optical quality along a broad concn. 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.
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    Garcia, F.; Korevaar, P. A.; Verlee, A.; Meijer, E. W.; Palmans, A. R. A.; Sanchez, L. The influence of [small pi]-conjugated moieties on the thermodynamics of cooperatively self-assembling tricarboxamides. Chem. Commun. 2013, 49, 8674– 8676,  DOI: 10.1039/c3cc43845g
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    The influence of π-conjugated moieties on the thermodynamics of cooperatively self-assembling tricarboxamides
    Garcia, Fatima; Korevaar, Peter A.; Verlee, Arno; Meijer, E. W.; Palmans, Anja R. A.; Sanchez, Luis
    Chemical Communications (Cambridge, United Kingdom) (2013), 49 (77), v8674-8676CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    A detailed investigation of the self-assembly behavior of C3-sym. tricarboxamides reveals that a larger π-conjugated core does not increase the stability of assemblies in an apolar solvent but makes the system more sensitive to destabilization by addn. of a good solvent.
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  49. 49
    Chan, A. K.-W.; Wong, K. M.-C.; Yam, V. W.-W. Supramolecular Assembly of Isocyanorhodium(I) Complexes: An Interplay of Rhodium(I)···Rhodium(I) Interactions, Hydrophobic–Hydrophobic Interactions, and Host–Guest Chemistry. J. Am. Chem. Soc. 2015, 137, 6920– 6931,  DOI: 10.1021/jacs.5b03396
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    Supramolecular Assembly of Isocyanorhodium(I) Complexes: An Interplay of Rhodium(I)···Rhodium(I) Interactions, Hydrophobic-Hydrophobic Interactions, and Host-Guest Chemistry
    Chan, Alan Kwun-Wa; Wong, Keith Man-Chung; Yam, Vivian Wing-Wah
    Journal of the American Chemical Society (2015), 137 (21), 6920-6931CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Tetrakis(isocyano)rhodium(I) complexes with different chain lengths of alkyl substituents were found to exhibit a strong tendency toward soln. state aggregation upon altering the concn., temp. and solvent compn. Temp.- and solvent-dependent UV-visible absorption studies were performed, and the data were analyzed using the aggregation model to elucidate the growth mechanism. The aggregation is found to involve extensive Rh(I)···Rh(I) interactions that are synergistically assisted by hydrophobic-hydrophobic interactions to give a rainbow array of soln. aggregate colors. The presence of three long alkyl substituents is crucial for the obsd. cooperativity in the aggregation. Mol. assemblies as nanoplates and nanovesicles were obsd. in the hexane-dichloromethane solvent mixts., arising from the different formation mechanisms based on the alkyl chain length of the complexes. Benzo-15-crown-5 moieties were incorporated for selective potassium ion binding to induce dimer formation and drastic color changes, rendering the system as potential colorimetric and luminescent cation sensors and as building blocks for ion-controlled supramol. assembly.
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  50. 50
    Valera, J. S.; Gómez, R.; Sánchez, L. Supramolecular Polymerization of [5]Helicenes. Consequences of Self-Assembly on Configurational Stability. Org. Lett. 2018, 20, 2020– 2023,  DOI: 10.1021/acs.orglett.8b00565
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    50
    Supramolecular Polymerization of [5]Helicenes. Consequences of Self-Assembly on Configurational Stability
    Valera, Jorge S.; Gomez, Rafael; Sanchez, Luis
    Organic Letters (2018), 20 (7), 2020-2023CODEN: ORLEF7; ISSN:1523-7052. (American Chemical Society)
    The supramol. polymn. of [5]helicenes I (1) and II (2) is investigated. The self-assembly of these helicenes proceeds by the operation of H-bonding interactions with a negligible participation of π-stacking. The enantiopurity of the sample has a dramatic effect on the supramol. polymn. mechanism since it reverts the isodesmic mechanism for the racemic mixt. to a cooperative one for the enantioenriched sample. Noticeably, the formation of supramol. polymers efficiently increases the configurational stability of 1,14-unsubstituted [5]helicenes.
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    Mayoral, M. J.; Guilleme, J.; Calbo, J.; Arago, J.; Aparicio, F.; Orti, E.; Torres, T.; Gonzalez-Rodriguez, D. Dual-Mode Chiral Self-Assembly of Cone-Shaped Subphthalocyanine Aromatics. J. Am. Chem. Soc. 2020, 142, 21017– 21031,  DOI: 10.1021/jacs.0c07291
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    Dual-Mode Chiral Self-Assembly of Cone-Shaped Subphthalocyanine Aromatics
    Mayoral, Maria J.; Guilleme, Julia; Calbo, Joaquin; Arago, Juan; Aparicio, Fatima; Orti, Enrique; Torres, Tomas; Gonzalez-Rodriguez, David
    Journal of the American Chemical Society (2020), 142 (50), 21017-21031CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Columnar polymers and liq. crystals obtained from π-conjugated cone-shaped mols. 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 mols. in soln. remains largely unexplored. Here, we show how a mol. geometry change, from flat to conic, can generate supramol. landscapes where different self-assembled species, each of them being under thermodn. equil. with the monomer, exist exclusively within distinct regimes. In particular, depending on the solvent nature - arom. or aliph. - cone-shaped C3-sym. subphthalocyanine 1 can undergo self-assembly either as a tail-to-tail dimer, showing monomer-dimer sigmoidal transitions, or as a head-to-tail noncentrosym. columnar polymer, exhibiting a nucleation-elongation polymn. mechanism. Moreover, the exptl. and theor. 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 assoc. with itself, but socially self-sort in the polymer regime, favoring an alternate stacking order along the columns.
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    Helmers, I.; Ghosh, G.; Albuquerque, R. Q.; Fernández, G. Pathway and Length Control of Supramolecular Polymers in Aqueous Media via a Hydrogen Bonding Lock. Angew. Chem., Int. Ed. 2021, 60, 4368– 4376,  DOI: 10.1002/anie.202012710
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    Pathway and Length Control of Supramolecular Polymers in Aqueous Media via a Hydrogen Bonding Lock
    Helmers, Ingo; Ghosh, Goutam; Albuquerque, Rodrigo Q.; Fernandez, Gustavo
    Angewandte Chemie, International Edition (2021), 60 (8), 4368-4376CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Programming the organization of π-conjugated systems into nanostructures of defined dimensions is a requirement for the prepn. of functional materials. Herein, we have achieved high-precision control over the self-assembly pathways and fiber length of an amphiphilic BODIPY dye in aq. media by exploiting a programmable hydrogen bonding lock. The presence of a (2-hydroxyethyl)amide group in the target BODIPY enables different types of intra- vs. intermol. hydrogen bonding, leading to a competition between kinetically controlled discoidal H-type aggregates and thermodynamically controlled 1D J-type fibers in water. The high stability of the kinetic state, which is dominated by the hydrophobic effect, is reflected in the slow transformation to the thermodn. product (several weeks at room temp.). However, this lag time can be suppressed by the addn. of seeds from the thermodn. species, enabling us to obtain supramol. polymers of tuneable length in water for multiple cycles.
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    Wu, A.; Isaacs, L. Self-Sorting: The Exception or the Rule?. J. Am. Chem. Soc. 2003, 125, 4831– 4835,  DOI: 10.1021/ja028913b
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    Self-Sorting: The Exception or the Rule?
    Wu, Anxin; Isaacs, Lyle
    Journal of the American Chemical Society (2003), 125 (16), 4831-4835CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    In this paper, we pose the question of whether self-sorting in designed systems is exceptional behavior or whether it is likely to become a more general phenomenon governing mol. recognition and self-assembly. To address this question we prepd. a mixt. comprising two of Davis' self-assembled ionophores, Rebek's tennis ball and calixarene tetraurea capsule, Meijer's ureidopyrimidinone, Reinhoudt's calixarene bis(rosette), and two mol. clips in CDCl3 soln. and obsd. the behavior of this ensemble by 1H NMR. As hypothesized, high-fidelity self-sorting behavior was obsd. The influence of several key variables - temp., concn., equil. consts., and the presence of competitors - on the fidelity of self-sorting is described. These results show that self-sorting is neither the exception nor the rule. They suggest, however, that the subset of known mol. aggregates that exceed the criteria required for thermodn. self-sorting is larger than previously appreciated and potentially quite broad.
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    Safont-Sempere, M. M.; Fernández, G.; Würthner, F. Self-Sorting Phenomena in Complex Supramolecular Systems. Chem. Rev. 2011, 111, 5784– 5814,  DOI: 10.1021/cr100357h
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    Self-Sorting Phenomena in Complex Supramolecular Systems
    Safont-Sempere, Marina M.; Fernandez, Gustavo; Wurthner, Frank
    Chemical Reviews (Washington, DC, United States) (2011), 111 (9), 5784-5814CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
    A review. In this review, the authors discuss the external variables and intrinsic factors (mol. codes) that influence the recognition or discrimination of supramolecularly interacting chem. species in soln. The comprehension of this "mol. programing" in artificial systems will define the variables that control self-sorting processes, and may ultimately contribute to a better understanding of the self-assembly pathways in natural systems.
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    Aratsu, K.; Prabhu, D. D.; Iwawaki, H.; Lin, X.; Yamauchi, M.; Karatsu, T.; Yagai, S. Self-sorting regioisomers through the hierarchical organization of hydrogen-bonded rosettes. Chem. Commun. 2016, 52, 8211– 8214,  DOI: 10.1039/C6CC03419E
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    Self-sorting regioisomers through the hierarchical organization of hydrogen-bonded rosettes
    Aratsu, Keisuke; Prabhu, Deepak D.; Iwawaki, Hidetaka; Lin, Xu; Yamauchi, Mitsuaki; Karatsu, Takashi; Yagai, Shiki
    Chemical Communications (Cambridge, United Kingdom) (2016), 52 (53), 8211-8214CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
    The self-assembly of two regioisomeric hydrogen-bonding naphthalenes was studied in mixed states in different polarity solvents. The regioisomers co-assemble to form heteromeric rosettes in chloroform. Upon injecting this soln. into methylcyclohexane the heteromeric rosettes kinetically form amorphous aggregates, which over time differentiate into thermodynamically stable distinct nanostructures through self-sorting.
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    Kitamoto, Y.; Pan, Z.; Prabhu, D. D.; Isobe, A.; Ohba, T.; Shimizu, N.; Takagi, H.; Haruki, R.; Adachi, S.-i.; Yagai, S. One-shot preparation of topologically chimeric nanofibers via a gradient supramolecular copolymerization. Nat. Commun. 2019, 10, 4578  DOI: 10.1038/s41467-019-12654-z
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    One-shot preparation of topologically chimeric nanofibers via a gradient supramolecular copolymerization
    Kitamoto Yuichi; Yagai Shiki; Pan Ziyan; Prabhu Deepak D; Isobe Atsushi; Yagai Shiki; Ohba Tomonori; Shimizu Nobutaka; Takagi Hideaki; Haruki Rie; Adachi Shin-Ichi
    Nature communications (2019), 10 (1), 4578 ISSN:.
    Supramolecular polymers have emerged in the last decade as highly accessible polymeric nanomaterials. An important step toward finely designed nanomaterials with versatile functions, such as those of natural proteins, is intricate topological control over their main chains. Herein, we report the facile one-shot preparation of supramolecular copolymers involving segregated secondary structures. By cooling non-polar solutions containing two monomers that individually afford helically folded and linearly extended secondary structures, we obtain unique nanofibers with coexisting distinct secondary structures. A spectroscopic analysis of the formation process of such topologically chimeric fibers reveals that the monomer composition varies gradually during the polymerization due to the formation of heteromeric hydrogen-bonded intermediates. We further demonstrate the folding of these chimeric fibers by light-induced deformation of the linearly extended segments.
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    Takahashi, S.; Yagai, S. Harmonizing Topological Features of Self-Assembled Fibers by Rosette-Mediated Random Supramolecular Copolymerization and Self-Sorting of Monomers by Photo-Cross-Linking. J. Am. Chem. Soc. 2022, 144, 13374– 13383,  DOI: 10.1021/jacs.2c05484
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    Harmonizing Topological Features of Self-Assembled Fibers by Rosette-Mediated Random Supramolecular Copolymerization and Self-Sorting of Monomers by Photo-Cross-Linking
    Takahashi, Sho; Yagai, Shiki
    Journal of the American Chemical Society (2022), 144 (29), 13374-13383CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Random copolymn. is an effective approach to synthesize the desired polymers by harmonizing distinct properties of different monomers. For supramol. polymers in which monomer binding is inherently dynamic, it is difficult to achieve random copolymn. of monomers with distinct mol. structures and properties due to an enthalpic advantage upon self-recognition (self-sorting). Herein, we demonstrate an example of thermodynamically controlled random supramol. copolymn. of two monomers functionalized with barbituric acid via the formation of six-membered hydrogen-bonded rosette intermediates to exhibit structural harmonization of the two main-chain motifs, i.e., intrinsically curved and linear motifs. One monomer based on naphthalene chromophore exclusively forms toroidal fibers, whereas another one bearing addnl. photoreactive diacetylene moiety affords linearly elongated fibers. Supramol. copolymn. of the two monomers is achieved by cooling hot monomer mixts. in a nonpolar solvent, which results in the formation of thermodynamically stable spirally folded yet elongated fibers. Atomic force microscopic observations and theor. simulations of the exptl. data obtained by absorption spectroscopy reveal the homopolymn. of the diacetylene-functionalized monomer in the high-temp. region, followed by the incorporation of the naphthalene monomer in the medium-temp. region to form supramol. copolymers with random monomer sequence. Finally, we demonstrate that the random copolymn. process can be switched to a narcissistically self-sorting one by deactivating monomer exchange through the photo-crosslinking of the diacetylene-functionalized monomers.
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    Kang, J.; Miyajima, D.; Mori, T.; Inoue, Y.; Itoh, Y.; Aida, T. A rational strategy for the realization of chain-growth supramolecular polymerization. Science 2015, 347, 646– 651,  DOI: 10.1126/science.aaa4249
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    A rational strategy for the realization of chain-growth supramolecular polymerization
    Kang, Jiheong; Miyajima, Daigo; Mori, Tadashi; Inoue, Yoshihisa; Itoh, Yoshimitsu; Aida, Takuzo
    Science (Washington, DC, United States) (2015), 347 (6222), 646-651CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    Over the past decade, major progress in supramol. polymn. has had a substantial effect on the design of functional soft materials. However, despite recent advances, most studies are still based on a preconceived notion that supramol. polymn. follows a step-growth mechanism, which precludes control over chain length, sequence, and stereochem. structure. Here we report the realization of chain-growth polymn. by designing metastable monomers with a shape-promoted intramol. hydrogen-bonding network. The monomers are conformationally restricted from spontaneous polymn. at ambient temps. but begin to polymerize with characteristics typical of a living mechanism upon mixing with tailored initiators. The chain growth occurs stereoselectively and therefore enables optical resoln. of a racemic monomer.
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    Haedler, A. T.; Meskers, S. C. J.; Zha, R. H.; Kivala, M.; Schmidt, H.-W.; Meijer, E. W. Pathway Complexity in the Enantioselective Self-Assembly of Functional Carbonyl-Bridged Triarylamine Trisamides. J. Am. Chem. Soc. 2016, 138, 10539– 10545,  DOI: 10.1021/jacs.6b05184
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    Pathway Complexity in the Enantioselective Self-Assembly of Functional Carbonyl-Bridged Triarylamine Trisamides
    Haedler, Andreas T.; Meskers, Stefan C. J.; Zha, R. Helen; Kivala, Milan; Schmidt, Hans-Werner; Meijer, E. W.
    Journal of the American Chemical Society (2016), 138 (33), 10539-10545CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Functional supramol. systems like carbonyl-bridged triarylamine (CBT) trisamides are known for their long-range energy transport at room temp. Understanding the complex self-assembly processes of this system allows for control over generated structures using controlled supramol. polymn. Here, we present two novel CBT trisamides with (S)- or (R)-chiral side chains which show a two-pathway self-assembly behavior in soln. Depending on the thermal profile during the self-assembly process, two different stable states are obtained under otherwise identical conditions. A kinetically trapped state A is reached upon cooling to 7 °C, via a proposed isodesmic process. In addn., there is a thermodynamically stable state B at 7 °C that is induced by first undercooling to -5 °C, via a nucleation-elongation mechanism. In both cases, helical supramol. aggregates comprising H-aggregated CBTs are formed. Addnl., controlled supramol. polymn. was achieved by mixing the two different states (A and B) from the same enantiomer, leading to a conversion of the kinetically trapped state to the thermodynamically stable state. This process is highly enantioselective, as no conversion is obsd. if the two states consist of opposite enantiomers. We thus show the importance and opportunities emerging from understanding the pathway complexity of functional supramol. systems.
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    Zhang, W.; Jin, W.; Fukushima, T.; Mori, T.; Aida, T. Helix Sense-Selective Supramolecular Polymerization Seeded by a One-Handed Helical Polymeric Assembly. J. Am. Chem. Soc. 2015, 137, 13792– 13795,  DOI: 10.1021/jacs.5b09878
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    Helix sense-selective supramolecular polymerization seeded by a one-handed helical polymeric assembly
    Zhang, Wei; Jin, Wusong; Fukushima, Takanori; Mori, Tadashi; Aida, Takuzo
    Journal of the American Chemical Society (2015), 137 (43), 13792-13795CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Helix sense-selective supramol. polymn. was achieved using a 1-handed helical nanotubular polymeric assembly as a seed. First, bipyridine (BPY)-appended achiral hexabenzocoronene (BPYHBC) was copolymd. noncovalently with chiral BPYHBCS (or BPYHBCR) at a molar ratio of 9:1, which, via the sergeants-and-soldiers effect, afforded a P-helical (or M-helical) nanotube, which was then treated with Cu2+ to transform into structurally robust (BPY)CuNT(P) (or (BPY)CuNT(M)) with a Cu2+/BPY coordination polymer shell. Helical seeds (BPY)CuNT(P) and (BPY)CuNT(M) brought about the controlled assembly of fluorinated chiral FHBCS and FHBCR as well as achiral FHBC to yield 1-handed helical nanotubular supramol. block copolymers, in which the helical senses of the newly formed block segments were solely detd. by those of the helical seeds employed. Noteworthy, FHBCS and FHBCR alone without the helical seeds form ill-defined agglomerates. Attempted supramol. polymn. of a racemic mixt. of FHBCS and FHBCR from (BPY)CuNT(P) (or (BPY)CuNT(M)) resulted in its chiral sepn., affording P-helical (or M-helical) diastereomeric block segments composed of FHBCS and FHBCR with different thermodn. properties.
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    Sarkar, S.; Sarkar, A.; George, S. J. Stereoselective Seed-Induced Living Supramolecular Polymerization. Angew. Chem., Int. Ed. 2020, 59, 19841– 19845,  DOI: 10.1002/anie.202006248
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    Stereoselective Seed-Induced Living Supramolecular Polymerization
    Sarkar, Souvik; Sarkar, Aritra; George, Subi J.
    Angewandte Chemie, International Edition (2020), 59 (45), 19841-19845CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Stereoselective and temporally controlled supramol. polymns. are ubiquitous in nature and are desirable attributes for the design of chiral, well-defined functional materials. Kinetically controlled, living supramol. polymn. (LSP) has emerged recently for the synthesis of supramol. polymers with controlled length and narrow dispersity. On the other hand, stringent design requirements for chiral-discriminating monomers precludes the stereoselective control of the supramol. polymer structure. Herein, a synergetic stereo- and structural control of supramol. polymn. by the realization of an unprecedented stereoselective seed-induced LSP is reported. Homochiral and seeded growth is demonstrated with bischromophoric naphthalene diimide (NDI) enantiomers with a chiral binaphthyl amine core, exhibiting strong self-recognition abilities and pathway complexity.
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    Sarkar, S.; Sarkar, A.; Som, A.; Agasti, S. S.; George, S. J. Stereoselective Primary and Secondary Nucleation Events in Multicomponent Seeded Supramolecular Polymerization. J. Am. Chem. Soc. 2021, 143, 11777– 11787,  DOI: 10.1021/jacs.1c05642
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    62
    Stereoselective Primary and Secondary Nucleation Events in Multicomponent Seeded Supramolecular Polymerization
    Sarkar, Souvik; Sarkar, Aritra; Som, Arka; Agasti, Sarit S.; George, Subi J.
    Journal of the American Chemical Society (2021), 143 (30), 11777-11787CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Bioinspired, kinetically controlled seeded growth has been recently shown to provide length, dispersity, and sequence control on the primary structure of dynamic supramol. polymers. However, command over the mol. organization at all hierarchical levels for the modulation of higher order structures of supramol. polymers remains a formidable task. In this context, a surface-catalyzed secondary nucleation process, which plays an important role in the autocatalytic generation of amyloid fibrils and also during the chiral crystn. of small monomers, offers exciting possibilities for topol. control in synthetic macromol. systems by introducing secondary growth pathways compared to the usual primary nucleation-elongation process. However, mechanistic insights into the mol. determinants and driving forces for the secondary nucleation event in synthetic systems are not yet realized. Herein, we attempt to fill this dearth by showing an unprecedented mol. chirality control on the primary and secondary nucleation events in seed-induced supramol. polymn. Comprehensive kinetic expts. using in situ spectroscopic probing of the temporal changes of the monomer organization during the growth process provide a unique study to characterize the primary and secondary nucleation events in a supramol. polymn. process. Kinetic analyses along with various microscopic studies further reveal the remarkable effect of stereoselective nucleation and seeding events on the (micro)structural aspects of the resulting multicomponent supramol. polymers.
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    Arja, K.; Selegård, R.; Paloncýová, M.; Linares, M.; Lindgren, M.; Norman, P.; Aili, D.; Nilsson, K. P. R. Self-Assembly of Chiro-Optical Materials from Nonchiral Oligothiophene-Porphyrin Derivatives and Random Coil Synthetic Peptides. ChemPlusChem 2023, 88, e202200262  DOI: 10.1002/cplu.202200262
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    Self-Assembly of Chiro-Optical Materials from Nonchiral Oligothiophene-Porphyrin Derivatives and Random Coil Synthetic Peptides
    Arja, Katriann; Selegaard, Robert; Paloncyova, Marketa; Linares, Mathieu; Lindgren, Mikael; Norman, Patrick; Aili, Daniel; Nilsson, K. Peter R.
    ChemPlusChem (2023), 88 (1), e202200262CODEN: CHEMM5; ISSN:2192-6506. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Biomimetic chiral optoelectronic materials can be utilized in electronic devices, biosensors and artificial enzymes. Herein, this work reports the chiro-optical properties and architectural arrangement of optoelectronic materials generated from self-assembly of initially nonchiral oligothiophene-porphyrin derivs. and random coil synthetic peptides. The photo-phys.- and structural properties of the materials were assessed by absorption-, fluorescence- and CD spectroscopy, as well as dynamic light scattering, SEM and theor. calcns. The materials display a three-dimensional ordered helical structure and optical activity that are obsd. due to an induced chirality of the optoelectronic element upon interaction with the peptide. Both these properties are influenced by the chem. compn. of the oligothiophene-porphyrin deriv., as well as the peptide sequence. We foresee that our findings will aid in developing self-assembled optoelectronic materials with dynamic architectonical accuracies, as well as offer the possibility to generate the next generation of materials for a variety of bioelectronic applications.
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    Zhang, L.; Zhang, G.; Qu, H.; Todarwal, Y.; Wang, Y.; Norman, P.; Linares, M.; Surin, M.; Zhang, H.-J.; Lin, J.; Jiang, Y.-B. Naphthodithiophene Diimide Based Chiral π-Conjugated Nanopillar Molecules. Angew. Chem., Int. Ed. 2021, 60, 24543– 24548,  DOI: 10.1002/anie.202107893
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    64
    Naphthodithiophene Diimide Based Chiral π-Conjugated Nanopillar Molecules
    Zhang, Li; Zhang, Guilan; Qu, Hang; Todarwal, Yogesh; Wang, Yun; Norman, Patrick; Linares, Mathieu; Surin, Mathieu; Zhang, Hui-Jun; Lin, Jianbin; Jiang, Yun-Bao
    Angewandte Chemie, International Edition (2021), 60 (46), 24543-24548CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    The synthesis, structures, and properties of [4]cyclonaphthodithiophene diimides ([4]C-NDTIs) are described. NDTIs as important n-type building blocks were catenated in the α-positions of thiophene rings via an unusual electrochem.-oxidn.-promoted macrocyclization route. The thiophene-thiophene junction in [4]C-NDTIs results in an ideal pillar shape. This interesting topol., along with appealing electronic and optical properties inherited from the NDTI units, endows the [4]C-NDTIs with both near-IR (NIR) light absorptions, strong excitonic coupling, and tight encapsulation of C60. Stable orientations of the NDTI units in the nanopillars lead to stable inherent chirality, which enables detailed CD studies on the impact of isomeric structures on π-conjugation. Remarkably, the [4]C-NDTIs maintain the strong π-π stacking abilities of NDTI units and thus adopt two-dimensional (2D) lattice arrays at the mol. level. These nanopillar mols. have great potential to mimic natural photosynthetic systems for the development of multifunctional org. materials.
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  • Abstract

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    Figure 1

    Figure 1. (a,b) Strategies to nanotube self-assembly through (a) the stacking of cyclic molecules or the folding of linear polymers or (b) the supramolecular polymerization of a molecule with two terminal binding sites that is able to assemble into cyclic entities or folded oligomers. (c) Chemical structure of dinucleobase monomers GC and AU. (d) Self-assembly of GC/AU. Watson–Crick pairing between complementary G:C and A:U nucleobases affords a mixture of H-bonded oligomers in equilibrium, among which an unstrained cyclic tetramer may be significantly stabilized if chelate cooperativity is strong enough. Polymerization through π–π stacking interactions and H-bonding between peripheral amides may then take place from these macrocycles (top) or from folded conformations of the linear oligomers (bottom), resulting, respectively, in stacked or coiled polymer nanotubes.

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    Figure 2

    Figure 2. Complete self-assembly of GC and AU. Self-assembly of GC (a–d) and AU (a′–d′) by progressively increasing the volume fraction of cyclohexane-D12 (Vcy; for 1H NMR studies) or heptane (Vhep) in mixtures with THF-D8 or THF, respectively, as monitored by (a,a′) 1H NMR at 5.0·10–4 M (please, see also Figure S1B), (b,b′) absorption, (c,c′) CD, or (d,d′) emission spectroscopies at 3.0·10–5 M. In the 1H NMR signal assignments, rod-shaped marks correspond to monomers or linear oligomeric species, while square-shaped marks correspond to cyclic tetramers. (e) Normalized CD changes at 429 nm at several concentrations as a function of Vhep for GC and AU at 298 K (αT = fraction of cyclotetramers, αN = fraction of nanotubes).

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    Figure 3

    Figure 3. Spectroscopic and morphological differences in the self-assembly of GC and AU. (a, b) CD trends recorded at 429 nm (GC) or 430 nm (AU) as a function of (a) the volume fraction of THF (VTHF = 1 – Vhep) in THF:heptane mixtures at 298 K or (b) the temperature in THF:heptane mixtures at Vhep = 0.97 ([GC] = 3.0·10–5 M (orange squares); [AU] = 8.0·10–6 M (green triangles)) or Vhep = 0.90 ([AU] = 3.0·10–5 M (green squares)). (c) Absorption, (d) emission, (e) CD, and (f) CPL spectra of the (GC)n and (AU)n polymers (solid lines) at Vhep = 0.99 compared to the GC and AU monomers (dashed lines) at Vhep = 0. (g, h) TEM images of the assemblies formed by (g) GC and (h) AU drop-cast from diluted solutions of high Vhep. (i) Nanotube diameter distributions measured by TEM.

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    Figure 4

    Figure 4. Self-sorting experiments. (a) Self-assembly of a 1:1 mixture of GC + AU by progressively increasing the volume fraction of cyclohexane-D12 (Vcy) in mixtures with THF-D8 monitored by 1H NMR ([GC] = [AU] = 2.0·10–3 M; T = 298 K; see also Figures S4A). The pictures at the right indicate approximately the distribution of supramolecular GC and AU species as Vcy is increased. Please compare with Figure 2, where the individual evolution of GC and AU is displayed. (b) Self-assembly of a 1:1 mixture of GC + AU by progressively increasing the volume fraction of heptane (Vhep) in mixtures with THF monitored by CD ([GC] = [AU] = 1.5·10–4 M; T = 298 K; see also Figures S4B). (c) Normalized CD changes at 435 nm as a function of Vhep for GC, AU, their mixture (spectra shown in panel (b)), and the arithmetic sum of GC+AU CD intensity taken from the isolated samples (αT = fraction of cyclotetramers, αN = fraction of nanotubes). (d) Self-assembly of a 1:3 mixture of GC + AU monitored by emission spectroscopy by progressively decreasing temperature in a THF:heptane mixture at Vhep = 0.9 ([GC] = 1.0·10–5 M; [AU] = 3.0·10–5 M; see also Figures S4C). (e) Normalized emission changes at 450 nm as a function of T for GC, AU, their mixture (spectra shown panel (d)), and the arithmetic sum of GC+AU emission intensity taken from the isolated samples.

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    Figure 5

    Figure 5. Simulations of supramolecular structures and spectra. Final structures of GC and AU nanotube models with molecular cores shown in magenta, A and G nitrogens in blue, and side chains as semitransparent green sticks. The nanotube models have opposite twist. The insets show the details of the nanotube core conformation. At each side, the CD spectra calculated as ensemble average over 10 snapshots extracted from the MD simulations is shown. The thin vertical lines show rotatory strengths from individual excited states. Units are arbitrary but comparable in between the two systems.

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    Figure 6

    Figure 6. Impact of chelate cooperativity on the self-assembly pathway and nanotube structure. Schematic representation of the whole supramolecular self-assembly process leading to nanotubes with the proposed stacked or folded internal structures. We simulate here the supramolecular scenarios encountered by GC (top panel) or AU (bottom panel) as Vhep is increased in THF:heptane mixtures and hence the intermolecular association strength, when going from left to right. In the middle, a simplified version of the panel shown in Figure 2e is reproduced, which shows the experimental evolution of the GC cyclotetramerization, AU polymerization, and GC polymerization with increasing Vhep. Each of the dashed frameworks at the top and the bottom provides a “snapshot” of the distribution of supramolecular species present in solution at 4 selected Vhep ranges before polymerization is triggered. Each of these frameworks contains the corresponding speciation curves in which the distribution of Watson–Crick H-bonded oligomers, which includes open oligomers from the dimer to the decamer (in blue), the cyclic tetramer (in green), and the monomer (in red), is simulated as a function of the total concentration. Orange and purple bands indicate, respectively, the concentration range employed in the 1H NMR and optical spectroscopy experiments performed in this work. Chelate cooperativity is several orders of magnitude higher for c(GC)4 than for c(AU)4. As a result, GC undergoes an “all-or-nothing” association process in which the cyclic tetramer is in equilibrium with the monomer, while AU mostly self-associates in a mixture of open (non-cyclic) species. As Vhep increases from left to right, the population of Watson–Crick H-bonded species increases until polymerization can be triggered at very high heptane contents (Vhep > 0.8). At this point, the c(GC)4 macrocycles are formed quantitatively in solution, whereas AU oligomers are long enough to become stabilized through folding interactions. Polymers originating from these two different situations can have a tubular structure with stacked or coiled molecular arrangements.

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  • References

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      Gong, Bing; Shao, Zhifeng
      Accounts of Chemical Research (2013), 46 (12), 2856-2866CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
      A review. The transport of mols. and ions across nanometer-scaled pores, created by natural or artificial mols., is a phenomenon of both fundamental and practical significance. Biol. channels are the most remarkable examples of mass transport across membranes and demonstrate nearly exclusive selectivity and high efficiency with a diverse collection of mols. These channels are crit. for many basic biol. functions, such as membrane potential, signal transduction, and osmotic homeostasis. If such highly specific and efficient mass transport or sepn. could be achieved with artificial nanostructures under controlled conditions, they could create revolutionary technologies in a variety of areas. For this reason, investigators from diverse disciplines have vigorously studied small non-deformable nanopores. The most exciting studies have focused on carbon nanotubes (CNTs), which have exhibited fast mass transport and high ion selectivity despite their very simple structure. However, the limitations of CNTs and the dearth of other small (≤2 nm) nanopores have severely hampered the systematic investigation of nanopore-mediated mass transport, which will be essential for designing artificial nanopores with desired functions en masse. Researchers can overcome the difficulties assocd. with CNT and other artificial pores by stacking macrocyclic building blocks with persistent shapes to construct tunable, self-assembling org. pores. This effort started when the authors discovered a highly efficient, one-pot macrocyclization process to efficiently prep. several classes of macrocycles with rigid backbones contg. non-deformable cavities. Such macrocycles, if stacked atop one another, should lead to nanotubular assemblies with defined inner pores detd. by their constituent macrocycles. One class of macrocycles with arom. oligoamide backbones had a very high propensity for directional assembly, forming nanotubular structures contg. nanometer and sub-nanometer hydrophilic pores. These self-assembling hydrophilic pores can form ion channels in lipid membranes with very large ion conductances. To control the assembly, the authors have further introduced multiple hydrogen-bonding side chains to enforce the stacking of rigid macrocycles into self-assembling nanotubes. This strategy has produced a self-assembling, sub-nanometer hydrophobic pore that not only acted as a transmembrane channel with surprisingly high ion selectivity, but also mediated a significant transmembrane water flux. The stacking of rigid macrocycles that can be chem. modified in either the lumen or the exterior surface can produce self-assembling org. nanotubes with inner pores of defined sizes. The combination of this approach with the availability and synthetic tunability of various rigid macrocycles should produce a variety of org. nanopores. Such structures would allow researchers to systematically explore mass transport in the sub-nanometer regime. Further advances should lead to novel applications such as biosensing, materials sepn., and mol. purifications.
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    10. 10
      Shimizu, L. S.; Salpage, S. R.; Korous, A. A. Functional Materials from Self-Assembled Bis-urea Macrocycles. Acc. Chem. Res. 2014, 47, 2116– 2127,  DOI: 10.1021/ar500106f
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      10
      Functional Materials from Self-Assembled Bis-urea Macrocycles
      Shimizu, Linda S.; Salpage, Sahan R.; Korous, Arthur A.
      Accounts of Chemical Research (2014), 47 (7), 2116-2127CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
      A review. This Account highlights the work from our labs. on bis-urea macrocycles constructed from two C-shaped spacers and two urea groups. These simple mol. units assembled with high fidelity into columnar structures guided by the three-centered urea hydrogen bonding motif and aryl stacking interactions. Individual columns are aligned and closely packed together to afford functional and homogeneous microporous crystals. This approach allows for precise and rational control over the dimensions of the columnar structure simply by changing the small mol. unit. When the macrocyclic unit lacks a cavity, columnar assembly gives strong pillars. Strong pillars with external functional groups such as basic lone pairs can expand like clays to accept guests between the pillars. Macrocycles that contain sizable interior cavities assemble into porous mol. crystals with aligned, well-defined columnar pores that are accessible to gases and guests. Herein, we examine the optimal design of the macrocyclic unit that leads to columnar assembly in high fidelity and probe the feasibility of incorporating a second functional group within the macrocycles. The porous mol. crystals prepd. through the self-assembly of bis-urea macrocycles display surface areas similar to zeolites but lower than MOFs. Their simple one-dimensional channels are well-suited for studying binding, investigating transport, diffusion and exchange, and monitoring the effects of encapsulation on reaction mechanism and product distribution. Guests that complement the size, shape, and polarity of the channels can be absorbed into these porous crystals with repeatable stoichiometry to form solid host-guest complexes. Heating or extn. with an org. solvent enables desorption or removal of the guest and subsequent recovery of the solid host. Further, these porous crystals can be used as containers for the selective [2 + 2] cycloaddns. of small enones such as 2-cyclohexenone or 3-methyl-cyclopentenone, while larger hosts bind and facilitate the photodimerization of coumarin. When the host framework incorporates benzophenone, a triplet sensitizer, UV-irradn. in the presence of oxygen efficiently generates singlet oxygen. Complexes of this host were employed to influence the selectivity of photooxidns. of 2-methyl-2-butene and cumene with singlet oxygen. Small systematic changes in the channel and bound reactants should enable systematic evaluation of the effects of channel dimensions, guest dimensions, and channel-guest interactions on the processes of absorption, diffusion, and reaction of guests within these nanochannels. Such studies could help in the development of new materials for sepns., gas storage, and catalysis.
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    11. 11
      Fuertes, A.; Juanes, M.; Granja, J. R.; Montenegro, J. Supramolecular functional assemblies: dynamic membrane transporters and peptide nanotubular composites. Chem. Commun. 2017, 53, 7861– 7871,  DOI: 10.1039/C7CC02997G
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      Supramolecular functional assemblies: dynamic membrane transporters and peptide nanotubular composites
      Fuertes, Alberto; Juanes, Marisa; Granja, Juan R.; Montenegro, Javier
      Chemical Communications (Cambridge, United Kingdom) (2017), 53 (56), 7861-7871CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
      A review on the recent development in supramol. chem. to help fabricate functional mol. devices, focusing on the prepn. of supramol. membrane transporters with special emphasis on the application of dynamic covalent bonds, and the prepn. of peptide nanotube hybrids with functional applications.
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    12. 12
      Picini, F.; Schneider, S.; Gavat, O.; Vargas Jentzsch, A.; Tan, J.; Maaloum, M.; Strub, J.-M.; Tokunaga, S.; Lehn, J.-M.; Moulin, E.; Giuseppone, N. Supramolecular Polymerization of Triarylamine-Based Macrocycles into Electroactive Nanotubes. J. Am. Chem. Soc. 2021, 143, 6498– 6504,  DOI: 10.1021/jacs.1c00623
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      12
      Supramolecular Polymerization of Triarylamine-Based Macrocycles into Electroactive Nanotubes
      Picini, Flavio; Schneider, Susanne; Gavat, Odile; Vargas Jentzsch, Andreas; Tan, Junjun; Maaloum, Mounir; Strub, Jean-Marc; Tokunaga, Shoichi; Lehn, Jean-Marie; Moulin, Emilie; Giuseppone, Nicolas
      Journal of the American Chemical Society (2021), 143 (17), 6498-6504CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      A S6-sym. triarylamine-based macrocycle (i.e., hexaaza[16]paracyclophane), decorated with six lateral amide functions, is synthesized by a convergent and modular strategy. This macrocycle is shown to undergo supramol. polymn. in o-dichlorobenzene, and its nanotubular structure is elucidated by a combination of spectroscopy and microscopy techniques, together with X-ray scattering and mol. modeling. Upon sequential oxidn., a spectroelectrochem. anal. of the supramol. polymer suggests an extended electronic delocalization of charge carriers both within the macrocycles (through bond) and between the macrocycles along the stacking direction (through space).
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    13. 13
      Bae, K.; Lee, D. G.; Khazi, M. I.; Kim, J. M. Stimuli-Responsive Polydiacetylene Based on the Self-Assembly of a Mercury-Bridged Macrocyclic Diacetylene Dimer. Macromolecules 2022, 55, 2882– 2891,  DOI: 10.1021/acs.macromol.1c02583
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      13
      Stimuli-Responsive Polydiacetylene Based on the Self-Assembly of a Mercury-Bridged Macrocyclic Diacetylene Dimer
      Bae, Kwangmin; Lee, Dong Geol; Khazi, Mohammed Iqbal; Kim, Jong-Man
      Macromolecules (Washington, DC, United States) (2022), 55 (7), 2882-2891CODEN: MAMOBX; ISSN:0024-9297. (American Chemical Society)
      The metal-mediated self-assembly process allows the well-directed and controlled construction of supramol. architectures, and the assembled metal-ligand complexes display diverse functionalities depending on the compn. of the complex template. Through the deliberate introduction of a metal-binding nucleobase, cytosine, to the macrocyclic diacetylene (MCDA), a macrocyclic ligand, CytMCDA, was synthesized. On account of the metal affinity of cytosine and the π-π interaction of the diacetylene template, a Hg-coordinated unidirectional columnar self-assembly of CytMCDA was generated that formed into org. nanotubes. The monomeric CytMCDA-Hg is covalently crosslinked to the blue-phase macrocyclic polydiacetylene nanotubes (CytMCPDA-Hg) via UV-induced topochem. polymn. CytMCPDA-Hg displayed a naked-eye-detectable sensing response toward heat and solvents with a brilliant blue-red chromatic transition. Moreover, owing to the high affinity of the mercury complex toward sulfur, CytMCPDA-Hg displayed a high sensitivity against thiols.
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    14. 14
      Roesner, E. K.; Asheghali, D.; Kirillova, A.; Strauss, M. J.; Evans, A. M.; Becker, M. L.; Dichtel, W. R. Arene–perfluoroarene interactions confer enhanced mechanical properties to synthetic nanotubes. Chem. Sci. 2022, 13, 2475– 2480,  DOI: 10.1039/D1SC05932G
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      14
      Arene-perfluoroarene interactions confer enhanced mechanical properties to synthetic nanotubes
      Roesner, Emily K.; Asheghali, Darya; Kirillova, Alina; Strauss, Michael J.; Evans, Austin M.; Becker, Matthew L.; Dichtel, William R.
      Chemical Science (2022), 13 (8), 2475-2480CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
      Supramol. nanotubes prepd. through macrocycle assembly offer unique properties that stem from their long-range order, structural predictability, and tunable microenvironments. However, assemblies that rely on weak non-covalent interactions often have limited aspect ratios and poor mech. integrity, which diminish their utility. Here pentagonal imine-linked macrocycles are prepd. by condensing a pyridine-contg. diamine and either terephthalaldehyde or 2,3,5,6-tetrafluoroterephthalaldehyde. Atomic force microscopy and synchrotron in solvo X-ray diffraction demonstrate that protonation of the pyridine groups drives assembly into high-aspect ratio nanotube assemblies. A 1 : 1 mixt. of each macrocycle yielded nanotubes with enhanced crystallinity upon protonation. UV-Vis and fluorescence spectroscopy indicate that nanotubes contg. both arene and perfluoroarene subunits display spectroscopic signatures of arene-perfluoroarene interactions. Touch-spun polymeric fibers contg. assembled nanotubes prepd. from the perhydro- or perfluorinated macrocycles exhibited Young's moduli of 1.09 and 0.49 GPa, resp. Fibers contg. nanotube assemblies reinforced by arene-perfluoroarene interactions yielded a 93% increase in the Young's modulus over the perhydro deriv., up to 2.1 GPa. These findings demonstrate that tuning the chem. compn. of the monomeric macrocycles can have profound effects on the mech. strength of the resulting assemblies. More broadly, these results will inspire future studies into tuning orthogonal non-covalent interactions between macrocycles to yield nanotubes with emergent functions and technol. potential.
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    15. 15
      Yashima, E.; Ousaka, N.; Taura, D.; Shimomura, K.; Ikai, T.; Maeda, K. Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions. Chem. Rev. 2016, 116, 13752– 13990,  DOI: 10.1021/acs.chemrev.6b00354
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      Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions
      Yashima, Eiji; Ousaka, Naoki; Taura, Daisuke; Shimomura, Kouhei; Ikai, Tomoyuki; Maeda, Katsuhiro
      Chemical Reviews (Washington, DC, United States) (2016), 116 (22), 13752-13990CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      A review. In this review, we describe the recent advances in supramol. helical assemblies formed from chiral and achiral small mols., oligomers (foldamers), and helical and nonhelical polymers from the viewpoints of their formations with unique chiral phenomena, such as amplification of chirality during the dynamic helically assembled processes, properties, and specific functionalities, some of which have not been obsd. in or achieved by biol. systems. In addn., a brief historical overview of the helical assemblies of small mols. and remarkable progress in the synthesis of single-stranded and multistranded helical foldamers and polymers, their properties, structures, and functions, mainly since 2009, will also be described.
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      Mayoral, M. J.; Bilbao, N.; González-Rodríguez, D. Hydrogen-Bonded Macrocyclic Supramolecular Systems in Solution and on Surfaces. ChemistryOpen 2016, 5, 10– 32,  DOI: 10.1002/open.201500171
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      Hydrogen-Bonded Macrocyclic Supramolecular Systems in Solution and on Surfaces
      Mayoral, Maria J.; Bilbao, Nerea; Gonzalez-Rodriguez, David
      ChemistryOpen (2016), 5 (1), 10-32CODEN: CHOPCK; ISSN:2191-1363. (Wiley-VCH Verlag GmbH & Co. KGaA)
      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 mol with two binding-sites. Taking advantage of intramol binding events, which are favored with respect to intermol binding in soln., can afford quant amts of a given supramol species under thermodn 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 soln or surface characterization techniques.
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      Aparicio, F.; Mayoral, M. J.; Montoro-García, C.; González-Rodríguez, D. Guidelines for the assembly of hydrogen-bonded macrocycles. Chem. Commun. 2019, 55, 7277– 7299,  DOI: 10.1039/C9CC03166A
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      Guidelines for the assembly of hydrogen-bonded macrocycles
      Aparicio F; Mayoral M J; Montoro-Garcia C; Gonzalez-Rodriguez D
      Chemical communications (Cambridge, England) (2019), 55 (51), 7277-7299 ISSN:.
      The formation of well-defined, discrete self-assembled architectures relies on the interplay between non-covalent interactions and cooperative phenomena. In particular, chelate or intramolecular cooperativity is responsible for the assembly of closed, cyclic structures in competition with open, linear oligomers, and it can be enhanced in several ways to increase the stability of a given cycle size. In this article, we review the work of several researchers on the synthesis of hydrogen-bonded macrocycles from ditopic molecules and analyze the main factors, often interrelated, that influence the equilibrium between ring and chain species. Emphasis will be set on the diverse features that can increase cyclization fidelity, including monomer geometry, template effects, conformational effects, intramolecular interactions and H-bonding pattern.
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      Chamorro, P. B.; Aparicio, F. Chiral nanotubes self-assembled from discrete non-covalent macrocycles. Chem. Commun. 2021, 57, 12712– 12724,  DOI: 10.1039/D1CC04968B
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      Chiral nanotubes self-assembled from discrete non-covalent macrocycles
      Chamorro, P. B.; Aparicio, F.
      Chemical Communications (Cambridge, United Kingdom) (2021), 57 (95), 12712-12724CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
      A review. Many strategies have been used to construct supramol. hollow tubes, including helical folding of oligomers, bundling of rod-like structures, rolling-up of sheets and stacking of covalent cycles. On the other hand, controlling chirality at the supramol. level continues attracting much interest because of its implications in future applications of porous systems. This review article covers the main examples in the literature that use simple mol. structures as chiral units for precise assembly into discrete non-covalent cyclic structures that are able to form chiral supramol. tubular systems.
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    19. 19
      Beingessner, R. L.; Fan, Y.; Fenniri, H. Molecular and supramolecular chemistry of rosette nanotubes. RSC Adv. 2016, 6, 75820– 75838,  DOI: 10.1039/C6RA16315G
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      Molecular and supramolecular chemistry of rosette nanotubes
      Beingessner, Rachel L.; Fan, Yiwen; Fenniri, Hicham
      RSC Advances (2016), 6 (79), 75820-75838CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)
      A review. The synthetic strategies, properties and applications of pyrimido[4,5-d]pyrimidine based rosette nanotubes were reviewed. A pyrimido[4,5-d]pyrimidine featuring the hydrogen bond donors and acceptors of both guanine (G) and cytosine (C) in the appropriate geometry was found to undergo hierarchical self-assembly into nanotubular architectures. Specifically, in soln. this heterocycle self-organized into cyclic hexamers through hydrogen bonding interactions, which then further π-π stack into rosette nanotubes (RNTs).
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    20. 20
      Stefan, L.; Monchaud, D. Applications of guanine quartets in nanotechnology and chemical biology. Nat. Rev. Chem. 2019, 3, 650– 668,  DOI: 10.1038/s41570-019-0132-0
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      Yagai, S.; Kitamoto, Y.; Datta, S.; Adhikari, B. Supramolecular Polymers Capable of Controlling Their Topology. Acc. Chem. Res. 2019, 52, 1325– 1335,  DOI: 10.1021/acs.accounts.8b00660
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      21
      Supramolecular Polymers Capable of Controlling Their Topology
      Yagai, Shiki; Kitamoto, Yuichi; Datta, Sougata; Adhikari, Bimalendu
      Accounts of Chemical Research (2019), 52 (5), 1325-1335CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
      One important class of supramol. materials is one-dimensionally elongated supramol. polymers, in which monomers are assocd. by reversible intermol. interactions, yielding a fibrous morphol. Unlike frequently reported conventional supramol. polymers based on, for instance, host-guest interactions, those composed of one-dimensionally stacked π-conjugated mols. can be encoded with high degrees of internal order by cooperative assocn. of the rigid arom. monomers, endowing such supramol. polymers with extraordinary properties and functionality. However, their internal order has not yet been exploited to manipulate the complex landscape of well-defined states of the supramol. polymer backbone, which may induce new functionalities beyond the intrinsic properties of the backbones.This Account will focus on the inceptive phase of our research on supramol. polymers with high degrees of internal order able to impart intrinsic curvature to their backbones. Initially, we developed a naphthalene mol. functionalized with barbituric acid, which forms uniform toroidal short fibers with diams. of approx. 16 nm via the formation of hydrogen-bonded cyclic hexamers (rosettes). As we thought the uniformity of the toroid size to arise from the intrinsic curvature generated upon stacking of the rosettes, we exploited this intrinsic curvature to design continuously curved extended supramol. polymers by extension of such mol. π-systems. The intrinsic curvature produced by the monomers with more expanded π-systems indeed gave us access to higher-order structures (topologies) ranging from randomly folded to helically folded coils in extended supramol. polymers. We will discuss the kinetic aspects of the generation of intrinsic curvature for topol. control, including the formation of toroidal structures resulting from ring-closing processes.For extended supramol. polymers with well-defined topologies, we will discuss manipulation of a complex landscape of well-defined states by external stimuli. The incorporation of a photoresponsive azobenzene chromophore in the original naphthalene mol. scaffold allowed us to reversibly destroy or recover the curvature of the main chain through trans-cis photoisomerization. By means of this photocontrollable curvature, we have demonstrated light-induced unfolding of helically folded structures into entirely stretched structures. Furthermore, a direct extension of the π-conjugated core provided us with access to unprecedented supramol. polymers with emergent time-dependent topol. transitions. Mols. with a naphthalene core conjugated with two phenylene units kinetically afforded supramol. polymers that consist of helically folded and misfolded domains. Upon aging the supramol. polymer soln., we obsd. spontaneous folding of the misfolded domains in a time scale of days, eventually obtaining a supramol. polymer topol. analogous to the tertiary structure of proteins. These supramol. polymers with unrivaled and active topologies provide new prospects for supramol. polymers as one-dimensional nanomaterials.
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    22. 22
      Jonkheijm, P.; Miura, A.; Zdanowska, M.; Hoeben, F. J. M.; De Feyter, S.; Schenning, A. P. H. J.; De Schryver, F. C.; Meijer, E. W. π-Conjugated Oligo-(p-phenylenevinylene) Rosettes and Their Tubular Self-Assembly. Angew. Chem., Int. Ed. 2004, 43, 74– 78,  DOI: 10.1002/anie.200352790
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      π-Conjugated oligo(p-phenylenevinylene) rosettes and their tubular self-assembly
      Jonkheijm, Pascal; Miura, Atsushi; Zdanowska, Magdalena; Hoeben, Freek J. M.; De Feyter, Steven; Schenning, Albertus P. H. J.; De Schryver, Frans C.; Meijer, E. W.
      Angewandte Chemie, International Edition (2004), 43 (1), 74-78CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Oligo(p-phenylenevinylene)s with pendant diaminotriazine moieties can self-assemble through hydrogen-bonding interactions to give hexameric rosettes. These rosettes further organize into large supramol. tubes with perfect space filling.
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    23. 23
      Schuster, G. B.; Cafferty, B. J.; Karunakaran, S. C.; Hud, N. V. Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA. J. Am. Chem. Soc. 2021, 143, 9279– 9296,  DOI: 10.1021/jacs.0c13081
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      23
      Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA
      Schuster, Gary B.; Cafferty, Brian J.; Karunakaran, Suneesh C.; Hud, Nicholas V.
      Journal of the American Chemical Society (2021), 143 (25), 9279-9296CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      A review. The hypothesis that RNA and DNA are products of chem. and biol. evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramol. polymers. These structures exhibit properties that provide robust solns. to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examn. by exptl. and computational methods provides insight into the chem. and phys. principles that govern a particular class of water-sol. one-dimensional supramol. polymers. In addn. to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of pos. charged, planar compds.; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent crosslinking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramol. structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-sol. supramol. polymers.
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    24. 24
      Tripathi, P.; Shuai, L.; Joshi, H.; Yamazaki, H.; Fowle, W. H.; Aksimentiev, A.; Fenniri, H.; Wanunu, M. Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors. J. Am. Chem. Soc. 2020, 142, 1680– 1685,  DOI: 10.1021/jacs.9b10993
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      24
      Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors
      Tripathi, Prabhat; Shuai, Liang; Joshi, Himanshu; Yamazaki, Hirohito; Fowle, William H.; Aksimentiev, Aleksei; Fenniri, Hicham; Wanunu, Meni
      Journal of the American Chemical Society (2020), 142 (4), 1680-1685CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Rosette nanotubes (RNTs) are a class of materials formed by mol. self-assembly of a fused guanine-cytosine base (G C base). An important feature of these self-assembled nanotubes is their precise at. structure, intriguing for rational design and optimization as synthetic transmembrane porins. Here, we present exptl. observations of ion transport across 1.1 nm inner diam. RNT porins (RNTPs) of various lengths in the range 5-200 nm. In a typical expt., custom lipophilic RNTPs were first inserted into lipid vesicles; the vesicles then spontaneously fused with a planar lipid bilayer, which produced stepwise increases of ion current across the bilayer. Our measurements in 1 M KCl soln. indicate ion transport rates of ∼50 ions s-1 V-1 m, which for short channels amts. to conductance values of ∼1 nS, commensurate with naturally occurring toxin channels such as α-hemolysin. Measurements of interaction times of α-cyclodextrin with RNTPs reveal two distinct unbinding time scales, which suggest that interactions of either face of α-cyclodextrin with the RNTP face are differentiable, backed with all-atom mol. dynamics simulations. Our results highlight the potential of RNTPs as self-assembled nonproteinaceous single-mol. sensors and selective nanofilters with tunable functionality through chem.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXltlWktQ%253D%253D&md5=a9c2f4ec874b0d1d0a3faf1c1e38cbb9
    25. 25
      Fukino, T.; Joo, H.; Hisada, Y.; Obana, M.; Yamagishi, H.; Hikima, T.; Takata, M.; Fujita, N.; Aida, T. Manipulation of Discrete Nanostructures by Selective Modulation of Noncovalent Forces. Science 2014, 344, 499– 504,  DOI: 10.1126/science.1252120
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      25
      Manipulation of Discrete Nanostructures by Selective Modulation of Noncovalent Forces
      Fukino, Takahiro; Joo, Hyunho; Hisada, Yuki; Obana, Maiko; Yamagishi, Hiroshi; Hikima, Takaaki; Takata, Masaki; Fujita, Norifumi; Aida, Takuzo
      Science (Washington, DC, United States) (2014), 344 (6183), 499-504CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      Ferrocene-based tetratopic pyridyl ligands, that can dynamically change their geometry by means of thermal rotation of their cyclopentadienyl rings in soln., has been obsd. to assemble with AgBF4 into discrete metal-org. nanotubes with large and uniform diams. The nanotubes could be cut into metal-org. nanorings through selective attenuation of the inter-nanoring interaction via ferrocene oxidn. The resultant nanorings could be transferred onto inorg. substrates electrostatically or allowed to reassemble to form the original nanotube by the reductive neutralization of their oxidized ferrocene units.
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    26. 26
      Huang, Z.; Kang, S.-K.; Banno, M.; Yamaguchi, T.; Lee, D.; Seok, C.; Yashima, E.; Lee, M. Pulsating Tubules from Noncovalent Macrocycles. Science 2012, 337, 1521– 1526,  DOI: 10.1126/science.1224741
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      26
      Pulsating Tubules from Noncovalent Macrocycles
      Huang, Zhegang; Kang, Seong-Kyun; Banno, Motonori; Yamaguchi, Tomoko; Lee, Dongseon; Seok, Chaok; Yashima, Eiji; Lee, Myongsoo
      Science (Washington, DC, United States) (2012), 337 (6101), 1521-1526CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      Despite recent advances in synthetic nanometer-scale tubular assembly, conferral of dynamic response characteristics to the tubules remains a challenge. Here, we report on supramol. nanotubules that undergo a reversible contraction-expansion motion accompanied by an inversion of helical chirality. Bent-shaped arom. amphiphiles self-assemble into hexameric macrocycles in aq. soln., forming chiral tubules by spontaneous one-dimensional stacking with a mutual rotation in the same direction. The adjacent arom. segments within the hexameric macrocycles reversibly slide along one another in response to external triggers, resulting in pulsating motions of the tubules accompanied by a chiral inversion. The arom. interior of the self-assembled tubules encapsulates hydrophobic guests such as carbon-60 (C60). Using a thermal trigger, we could regulate the C60-C60 interactions through the pulsating motion of the tubules.
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    27. 27
      Tashiro, K.; Saito, T.; Arima, H.; Suda, N.; Vedhanarayanan, B.; Yagai, S. Scissor-Shaped Photochromic Dyads: Hierarchical Self-Assembly and Photoresponsive Property. Chem. Rec. 2022, 22, e202100252  DOI: 10.1002/tcr.202100252
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      27
      Scissor-Shaped Photochromic Dyads: Hierarchical Self-Assembly and Photoresponsive Property
      Tashiro, Keigo; Saito, Takuho; Arima, Hironari; Suda, Natsuki; Vedhanarayanan, Balaraman; Yagai, Shiki
      Chemical Record (2022), 22 (2), e202100252CODEN: CRHEAK; ISSN:1528-0691. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Unique relationships between hierarchically organized biol. nanostructures and functions have motivated chemists to construct sophisticated artificial nanostructured systems from small and simple synthetic mols. through self assembly. As one of such sophisticated systems, we have investigated scissor shaped photochromic dyads that can hierarchically self assemble into discrete nanostructures showing photoresponsive properties. We synthesized various azobenzene dyads and found that these dyads adopt intramolecularly folded conformation like a closed scissor, and then self assemble into toroidal nanostructures by generating curvature. The toroids further organize into nanotubes and further into helical supramol. fibers depending on the nature of alkyl substituents. All of these nanostructures can be dissocd. and reorganized through the photoisomerization of azobenzene units. On the other hand, the introduction of stilbene chromophores instead of azobenzenes leads to one-dimensional supramol. polymn., which upon the intramol. photocyclization of stilbene chromophores shifts to curved self assembly leading to helicoidal fibers with distinct supramol. chirality.
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    28. 28
      Shi, Q.; Javorskis, T.; Bergquist, K.-E.; Ulčinas, A.; Niaura, G.; Matulaitienė, I.; Orentas, E.; Wärnmark, K. Stimuli-controlled self-assembly of diverse tubular aggregates from one single small monomer. Nat. Commun. 2017, 8, 14943  DOI: 10.1038/ncomms14943
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      Stimuli-controlled self-assembly of diverse tubular aggregates from one single small monomer
      Shi, Qixun; Javorskis, Tomas; Bergquist, Karl-Erik; Ulcinas, Arturas; Niaura, Gediminas; Matulaitiene, Ieva; Orentas, Edvinas; Waernmark, Kenneth
      Nature Communications (2017), 8 (), 14943pp.CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
      The design and synthesis of new stimuli-responsive hydrogen-bonding monomers that display a diversity of self-assembly pathways is of central importance in supramol. chem. Here we describe the aggregation properties of a simple, intrinsically C2-sym. enantiopure bicyclic cavity compd. bearing a terminally unsubstituted ureidopyrimidinone fragment fused with a pyrrole moiety in different solvents and in the absence and presence of C60 and C70 guests. The tetrameric cyclic aggregate is selectively obtained in chlorinated solvents, where only part of the available hydrogen bonding sites are utilized, whereas in toluene or upon addn. of C70 guests, further aggregation into tubular supramol. polymers is achieved. The open-end cyclic assemblies rearrange into a closed-shell capsule upon introduction of C60 with an accompanied symmetry breaking of the monomer. Our study demonstrates that a C60 switch can be used to simultaneously control the topol. and occupancy of tubular assemblies resulting from the aggregation of small monomers.
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    29. 29
      Liu, C.-Z.; Yan, M.; Wang, H.; Zhang, D.-W.; Li, Z.-T. Making Molecular and Macromolecular Helical Tubes: Covalent and Noncovalent Approaches. ACS Omega 2018, 3, 5165– 5176,  DOI: 10.1021/acsomega.8b00681
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      29
      Making Molecular and Macromolecular Helical Tubes: Covalent and Noncovalent Approaches
      Liu, Chuan-Zhi; Yan, Meng; Wang, Hui; Zhang, Dan-Wei; Li, Zhan-Ting
      ACS Omega (2018), 3 (5), 5165-5176CODEN: ACSODF; ISSN:2470-1343. (American Chemical Society)
      Areview. Arom. foldamers possess well-defined cavity that can be stabilized by discrete intramol. interactions including hydrogen bonding, solvophobicity, electrostatic repulsion, or coordination. Long foldamers can form dynamic deep helical tubular architectures that are not only structurally attractive but also useful hosts for guest encapsulation, chirality induction, delivery, and catalysis. This kind of helical tubular structures can be formed by single mols. or macromols. or by connecting short-folded or helical segments through noncovalent or covalent forces. This perspective summarizes the recent advances on the construction of helical tubes and their properties and functions.
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    30. 30
      Balbo Block, M. A.; Kaiser, C.; Khan, A.; Hecht, S. Discrete Organic Nanotubes Based on a Combination of Covalent and Non-Covalent Approaches. In Functional Molecular Nanostructures; Schlüter, A. D., Ed.; Springer Berlin Heidelberg: Berlin, Heidelberg, 2005; pp 89– 150.
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      Vázquez-González, V.; Mayoral, M. J.; Chamorro, R.; Hendrix, M. M. R. M.; Voets, I. K.; González-Rodríguez, D. Noncovalent Synthesis of Self-Assembled Nanotubes through Decoupled Hierarchical Cooperative Processes. J. Am. Chem. Soc. 2019, 141, 16432– 16438,  DOI: 10.1021/jacs.9b07868
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      31
      Noncovalent Synthesis of Self-Assembled Nanotubes through Decoupled Hierarchical Cooperative Processes
      Vazquez-Gonzalez, Violeta; Mayoral, Maria J.; Chamorro, Raquel; Hendrix, Marco M. R. M.; Voets, Ilja K.; Gonzalez-Rodriguez, David
      Journal of the American Chemical Society (2019), 141 (41), 16432-16438CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Because of their wide no. of biol. functions and potential applications, self-assembled nanotubes constitute highly relevant targets in noncovalent synthesis. Herein, we introduce a novel approach to produce supramol. nanotubes with defined inner and outer diams. 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 polymn.
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    32. 32
      Vázquez-González, V.; Mayoral, M. J.; Aparicio, F.; Martinez-Arjona, P.; Gonzalez-Rodriguez, D. The Role of Peripheral Amide Groups as Hydrogen-Bonding Directors in the Tubular Self-Assembly of Dinucleobase Monomers. ChemPlusChem 2021, 86, 1087– 1096,  DOI: 10.1002/cplu.202100255
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      The Role of Peripheral Amide Groups as Hydrogen-Bonding Directors in the Tubular Self-Assembly of Dinucleobase Monomers
      Vazquez-Gonzalez, Violeta; Mayoral, Maria J.; Aparicio, Fatima; Martinez-Arjona, Paula; Gonzalez-Rodriguez, David
      ChemPlusChem (2021), 86 (8), 1087-1096CODEN: CHEMM5; ISSN:2192-6506. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Nanotubes are a fascinating kind of self-assembled structure which have a wide interest and potential in supramol. chem. We demonstrated that nanotubes of defined dimensions can be produced from dinucleobase monomers through two decoupled hierarchical cooperative processes: cyclotetramerization and supramol. polymn. 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 1H NMR and CD spectroscopy techniques allowed us to analyze quant. the thermodn. of each of these two processes sep. We found out that the presence of these amide directors is essential to guide the polymn. event and that their nature and no. have a strong influence, not only on the stabilization of the stacks of macrocycles, but also on the supramol. polymn. mechanism.
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      Aparicio, F.; Chamorro, P. B.; Chamorro, R.; Casado, S.; González-Rodríguez, D. Nanostructured Micelle Nanotubes Self-Assembled from Dinucleobase Monomers in Water. Angew. Chem., Int. Ed. 2020, 59, 17091– 17096,  DOI: 10.1002/anie.202006877
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      Nanostructured Micelle Nanotubes Self-Assembled from Dinucleobase Monomers in Water
      Aparicio, Fatima; Chamorro, Paula B.; Chamorro, Raquel; Casado, Santiago; Gonzalez-Rodriguez, David
      Angewandte Chemie, International Edition (2020), 59 (39), 17091-17096CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Despite the central importance of aq. amphiphile assemblies in science and industry, the size and shape of these nano-objects is often difficult to control with accuracy owing to the non-directional nature of the hydrophobic interactions that sustain them. Here, using a bioinspired strategy that consists of programming an amphiphile with shielded directional Watson-Crick hydrogen-bonding functions, its self-assembly in water was guided toward a novel family of chiral micelle nanotubes with partially filled lipophilic pores of about 2 nm in diam. Moreover, these tailored nanotubes are successfully demonstrated to ext. and host mols. that are complementary in size and chem. affinity.
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    34. 34
      Chamorro, P. B.; Aparicio, F.; Chamorro, R.; Bilbao, N.; Casado, S.; González-Rodríguez, D. Exploring the tubular self-assembly landscape of dinucleobase amphiphiles in water. Org. Chem. Front. 2021, 8, 686– 696,  DOI: 10.1039/D0QO01110J
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      Exploring the tubular self-assembly landscape of dinucleobase amphiphiles in water
      Chamorro, Paula B.; Aparicio, Fatima; Chamorro, Raquel; Bilbao, Nerea; Casado, Santiago; Gonzalez-Rodriguez, David
      Organic Chemistry Frontiers (2021), 8 (4), 686-696CODEN: OCFRA8; ISSN:2052-4129. (Royal Society of Chemistry)
      The design and prodn. of the next generations of synthetic aq. self-assembled systems able to mimic some biol. features will require increasingly sophisticated monomer constituents that make use of addnl. interactions to hydrophibic effects to attain enhanced structural and functional complexity. Here, we broadly investigate the aq. self-assembly of dinucleobase amphiphilic monomers into helical nanotubes under a wide range of different conditions of temp., concn., solvent compn. and pH. Such monomers comprise an amphiphilic π-conjugated central block, endowed with a lipophilic chiral tail and a hydrophilic group that can be made anionic (carboxylate), neutral (glycol) or cationic (ammonium), disubstituted with complementary guanine and cytosine nucleobases at each termini. These mols. self-assemble into amphiphilic nanotubes in water but, when subjected to diverse (drastic) changes in the exptl. conditions, undergo either disassembly into monomers, chiral reorganization, or a morphol. restructuration into globular objects due to dehydration of the peripheral hydrophilic groups.
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    35. 35
      Montoro-García, C.; Camacho-García, J.; López-Pérez, A. M.; Bilbao, N.; Romero-Pérez, S.; Mayoral, M. J.; González-Rodríguez, D. High-Fidelity Noncovalent Synthesis of Hydrogen-Bonded Macrocyclic Assemblies. Angew. Chem., Int. Ed. 2015, 54, 6780– 6784,  DOI: 10.1002/anie.201501321
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      High-Fidelity Noncovalent Synthesis of Hydrogen-Bonded Macrocyclic Assemblies
      Montoro-Garcia, Carlos; Camacho-Garcia, Jorge; Lopez-Perez, Ana M.; Bilbao, Nerea; Romero-Perez, Sonia; Mayoral, Maria J.; Gonzalez-Rodriguez, David
      Angewandte Chemie, International Edition (2015), 54 (23), 6780-6784CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      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 thermodn. and kinetic stability and is formed with high fidelities within a broad concn. range.
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    36. 36
      Montoro-García, C.; Camacho-García, J.; López-Pérez, A. M.; Mayoral, M. J.; Bilbao, N.; González-Rodríguez, D. Role of the Symmetry of Multipoint Hydrogen Bonding on Chelate Cooperativity in Supramolecular Macrocyclization Processes. Angew. Chem., Int. Ed. 2016, 55, 223– 227,  DOI: 10.1002/anie.201508854
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      Role of the Symmetry of Multipoint Hydrogen Bonding on Chelate Cooperativity in Supramolecular Macrocyclization Processes
      Montoro-Garcia, Carlos; Camacho-Garcia, Jorge; Lopez-Perez, Ana M.; Mayoral, Maria J.; Bilbao, Nerea; Gonzalez-Rodriguez, David
      Angewandte Chemie, International Edition (2016), 55 (1), 223-227CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Herein, the authors analyze the intrinsic chelate effect that multipoint H-bonding patterns exert on the overall energy of dinucleoside cyclic systems. 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 unsym. ADD-DAA or DDA-AAD patterns to the sym. DAD-ADA pattern.
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    37. 37
      Jorgensen, W. L.; Pranata, J. Importance of secondary interactions in triply hydrogen bonded complexes: guanine-cytosine vs uracil-2,6-diaminopyridine. J. Am. Chem. Soc. 1990, 112, 2008– 2010,  DOI: 10.1021/ja00161a061
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      Importance of secondary interactions in triply hydrogen bonded complexes: guanine-cytosine vs uracil-2,6-diaminopyridine
      Jorgensen, William L.; Pranata, Julianto
      Journal of the American Chemical Society (1990), 112 (5), 2008-10CODEN: JACSAT; ISSN:0002-7863.
      Although complexes of guanine-cytosine and uracil-2,6-diaminopyridine are both triply H-bonded in CHCl3, measured assocn. consts. for such systems vary by 102-103. The origin of the discrepancy is analyzed here through computational studies. Monte Carlo statistical mechanics simulations for the complexes in CHCl3 also find the substantial binding preference for guanine-cytosine. The difference is then traced to the gas-phase interaction energies which favor guanine-cytosine complexation by ca. 10 kcal/mol. The three H bonds are of the same type in both complexes; however, the variation in their arrangement leads to secondary electrostatic effects that account for the destabilization of the uracil-2,6-diaminopyridine complex. Such secondary interactions are a significant element for consideration in mol. design.
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      Camacho-García, J.; Montoro-García, C.; López-Perez, A. M.; Bilbao, N.; Romero-Pérez, S.; González-Rodríguez, D. Synthesis and complementary self-association of novel lipophilic [small pi]-conjugated nucleoside oligomers. Org. Biomol. Chem. 2015, 13, 4506– 4513,  DOI: 10.1039/C5OB00098J
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      Synthesis and complementary self-association of novel lipophilic π-conjugated nucleoside oligomers
      Camacho-Garcia, J.; Montoro-Garcia, C.; Lopez-Perez, A. M.; Bilbao, N.; Romero-Perez, S.; Gonzalez-Rodriguez, D.
      Organic & Biomolecular Chemistry (2015), 13 (15), 4506-4513CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)
      A series of lipophilic nucleosides comprising natural and non-natural bases that are π-conjugated to a short oligo-phenylene-ethynylene fragment has been synthesized. These bases comprise guanosine, isoguanosine, and 2-amino-adenosine as purine heterocycles, and cytidine, iso-cytosine and uridine as complementary pyrimidine bases. The hydrogen-bonding dimerization and assocn. processes between complementary bases were also studied by 1H NMR and absorption spectroscopy in order to obtain the relevant assocn. consts.
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    39. 39
      Mayoral, M. J.; Camacho-Garcia, J.; Magdalena-Estirado, E.; Blanco-Lomas, M.; Fadaei, E.; Montoro-Garcia, C.; Serrano-Molina, D.; Gonzalez-Rodriguez, D. Dye-conjugated complementary lipophilic nucleosides as useful probes to study association processes by fluorescence resonance energy transfer. Org. Biomol. Chem. 2017, 15, 7558– 7565,  DOI: 10.1039/C7OB01930K
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      Dye-conjugated complementary lipophilic nucleosides as useful probes to study association processes by fluorescence resonance energy transfer
      Mayoral, M. J.; Camacho-Garcia, J.; Magdalena-Estirado, E.; Blanco-Lomas, M.; Fadaei, E.; Montoro-Garcia, C.; Serrano-Molina, D.; Gonzalez-Rodriguez, D.
      Organic & Biomolecular Chemistry (2017), 15 (36), 7558-7565CODEN: OBCRAK; ISSN:1477-0520. (Royal Society of Chemistry)
      Modern supramol. chem. relies on the combination of diverse anal. techniques that can provide complementary information on complex self-assembly landscapes. Among them, resonance energy transfer, monitored by fluorescence emission spectroscopy, arises as a sensitive and convenient phenomenon to report binding intermol. interactions. The use of mol. probes labeled with suitable complementary energy-transfer pairs can provide valuable information about the thermodn., kinetics and self-sorting characteristics of a particular self-assembled system. The objective of this work is to generate a set of nucleoside FRET probes that can be reliably employed to prove and analyze quant. H-bonding interactions between complementary Watson-Crick pairs. We first describe the prepn. of a set of lipophilic nucleosides that are linked to a π-conjugated functional fragment. The bases include guanosine and 2-aminoadenosine as purine heterocycles, and cytidine and uridine as complementary pyrimidine bases. The π-conjugated moiety comprises either a short phenylene-ethynylene oligomer, a bithiophene, or a BODIPY dye. We then demonstrate that the last two chromophores constitute an energy donor-acceptor couple and that donor emission quenching can be related to the ratio of mols. bound to the complementary acceptor pair. Hence, fluorescence spectroscopy in combination with resonance energy transfer, is shown here to be a useful tool to study and quantify the assocn. and self-sorting events between complementary and non-complementary nucleosides in apolar arom. solvents, where the binding strength is considerably high, and sensitive techniques that employ low concns. are demanded.
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      Serrano-Molina, D.; de Juan, A.; González-Rodríguez, D. Dinucleoside-Based Macrocycles Displaying Unusually Large Chelate Cooperativities. Chem. Rec. 2021, 21, 480– 497,  DOI: 10.1002/tcr.202000141
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      40
      Dinucleoside-based Macrocycles Displaying Unusually Large Chelate Cooperativities
      Serrano-Molina, David; de Juan, Alberto; Gonzalez-Rodriguez, David
      Chemical Record (2021), 21 (3), 480-497CODEN: CRHEAK; ISSN:1528-0691. (Wiley-VCH Verlag GmbH & Co. KGaA)
      A review. High-fidelity prodn. of a single self-assembled species in competition with others relies on achieving strong chelate cooperativities, which can be quantified by the effective molarity parameter. Therefore, supramol. systems displaying very high effective molarities are reliably formed in a wide range of exptl. conditions and exhibit "all-or-none" phenomena, meaning that the assembly is either fully formed or fully dissocd. into the corresponding monomeric components. We summarize here our efforts in the study and characterization of one of these synthetic systems exhibiting record chelate cooperativities: the self-assembly of rod-like dinucleoside mols. into tetrameric macrocycles through hydrogen-bonding Watson-Crick interactions.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXislShu7bN&md5=0eea5b2c6ebc4d57961031c2517004fc
    41. 41
      Romero-Pérez, S.; Camacho-García, J.; Montoro-García, C.; López-Pérez, A. M.; Sanz, A.; Mayoral, M. J.; González-Rodríguez, D. G-Arylated Hydrogen-Bonded Cyclic Tetramer Assemblies with Remarkable Thermodynamic and Kinetic Stability. Org. Lett. 2015, 17, 2664– 2667,  DOI: 10.1021/acs.orglett.5b01042
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      41
      G-Arylated Hydrogen-Bonded Cyclic Tetramer Assemblies with Remarkable Thermodynamic and Kinetic Stability
      Romero-Perez, Sonia; Camacho-Garcia, Jorge; Montoro-Garcia, Carlos; Lopez-Perez, Ana M.; Sanz, Alfredo; Mayoral, Maria Jose; Gonzalez-Rodriguez, David
      Organic Letters (2015), 17 (11), 2664-2667CODEN: ORLEF7; ISSN:1523-7052. (American Chemical Society)
      The prepn. and self-assembly of novel G-C dinucleoside monomers that are equipped with electron-poor aryl groups at the G-N2 amino group have been studied. Such monomers assoc. via Watson-Crick H-bonding into discrete unstrained tetrameric macrocycles that arise as a thermodynamically and kinetically stabilized product in a wide variety of exptl. conditions, including very polar solvent environments and low concns. G-arylation produces an increased stability of the cyclic assembly, as a result of a subtle interplay between enthalpic and entropic effects involving the solvent coordination sphere.
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    42. 42
      Montoro-García, C.; Mayoral, M. J.; Chamorro, R.; González-Rodríguez, D. How Large Can We Build a Cyclic Assembly? Impact of Ring Size on Chelate Cooperativity in Noncovalent Macrocyclizations. Angew. Chem., Int. Ed. 2017, 56, 15649– 15653,  DOI: 10.1002/anie.201709563
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      42
      How Large Can We Build a Cyclic Assembly? Impact of Ring Size on Chelate Cooperativity in Noncovalent Macrocyclizations
      Montoro-Garcia, Carlos; Mayoral, Maria J.; Chamorro, Raquel; Gonzalez-Rodriguez, David
      Angewandte Chemie, International Edition (2017), 56 (49), 15649-15653CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Self-assembled systems rely on intramol. 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 assoc. in cyclic tetramers by complementary Watson-Crick H-bonding interactions. As the monomer length increases, and thus the no. of C(sp)-C(sp2) σ-bonds in the π-conjugated skeleton, the macrocycle stability decreases due to a notable redn. in effective molarity (EM), which has a clear entropic origin. We detd. the relationship between EM or ΔS and the no. of σ-bonds, which allowed us to predict the max. monomer lengths at which cyclic species would still assemble quant., or whether the cyclic species would not able to compete at all with linear oligomers over the whole concn. range.
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    43. 43
      Montoro-García, C.; Bilbao, N.; Tsagri, I. M.; Zaccaria, F.; Mayoral, M. J.; Fonseca Guerra, C.; González-Rodríguez, D. Impact of Conformational Effects on the Ring–Chain Equilibrium of Hydrogen-Bonded Dinucleosides. Chem.–Eur. J. 2018, 24, 11983– 11991,  DOI: 10.1002/chem.201801704
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      Impact of Conformational Effects on the Ring-Chain Equilibrium of Hydrogen-Bonded Dinucleosides
      Montoro-Garcia, Carlos; Bilbao, Nerea; Tsagri, Iris M.; Zaccaria, Francesco; Mayoral, Maria J.; Fonseca Guerra, Celia; Gonzalez-Rodriguez, David
      Chemistry - A European Journal (2018), 24 (46), 11983-11991CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Supramol. ring-vs.-chain equil. are ubiquitous in biol. 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 mol. 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 equil., such as steric hindrance, intramol. interactions, or π-conjugation pathways.
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    44. 44
      Mayoral, M. J.; Serrano-Molina, D.; Camacho-García, J.; Magdalena-Estirado, E.; Blanco-Lomas, M.; Fadaei, E.; González-Rodríguez, D. Understanding complex supramolecular landscapes: non-covalent macrocyclization equilibria examined by fluorescence resonance energy transfer. Chem. Sci. 2018, 9, 7809– 7821,  DOI: 10.1039/C8SC03229G
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      Understanding complex supramolecular landscapes: non-covalent macrocyclization equilibria examined by fluorescence resonance energy transfer
      Mayoral, Maria J.; Serrano-Molina, David; Camacho-Garcia, Jorge; Magdalena-Estirado, Eva; Blanco-Lomas, Marina; Fadaei, Elham; Gonzalez-Rodriguez, David
      Chemical Science (2018), 9 (40), 7809-7821CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
      As mol. self-assembled systems increase in complexity, due to a large no. of participating entities and/or the establishment of multiple competing equil., their full understanding becomes likewise more complicated, and the use of diverse anal. 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 thermodn. data about complex supramol. 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 intermol. assocn. processes of Watson-Crick H-bonding pairs. Multiwavelength anal. of the monomer emission changes allowed us to det. cyclotetramerization consts. 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 expts., fluorescence and CD spectroscopy measurements in different regions of the visible spectrum addnl. reveal intermol. 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.
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    45. 45
      Serrano-Molina, D.; Montoro-García, C.; Mayoral, M. J.; de Juan, A.; González-Rodríguez, D. Self-Sorting Governed by Chelate Cooperativity. J. Am. Chem. Soc. 2022, 144, 5450– 5460,  DOI: 10.1021/jacs.1c13295
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      45
      Self-Sorting Governed by Chelate Cooperativity
      Serrano-Molina, David; Montoro-Garcia, Carlos; Mayoral, Maria J.; de Juan, Alberto; Gonzalez-Rodriguez, David
      Journal of the American Chemical Society (2022), 144 (12), 5450-5460CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Self-sorting phenomena are the basis of manifold relevant (bio)chem. processes where a set of mols. is able to interact with no interference from other sets and are ruled by a no. of codes that are programmed in mol. structures. In this work, we study, the relevance of chelate cooperativity as a code for achieving high self-sorting fidelity. In particular, we establish qual. and quant. relationships between the cooperativity of a cyclic system and the self-sorting fidelity when combined with other mols. that share identical geometry and/or binding interactions. We demonstrate that only systems displaying sufficiently strong chelate cooperativity can achieve quant. narcissistic self-sorting fidelities either by dictating the distribution of cyclic species in complex mixts. or by ruling the competition between the intra- and intermol. versions of a noncovalent interaction.
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    46. 46
      Bilbao, N.; Destoop, I.; De Feyter, S.; González-Rodríguez, D. Two-Dimensional Nanoporous Networks Formed by Liquid-to-Solid Transfer of Hydrogen-Bonded Macrocycles Built from DNA Bases. Angew. Chem., Int. Ed. 2016, 55, 659– 663,  DOI: 10.1002/anie.201509233
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      Two-Dimensional Nanoporous Networks Formed by Liquid-to-Solid Transfer of Hydrogen-Bonded Macrocycles Built from DNA Bases
      Bilbao, Nerea; Destoop, Iris; De Feyter, Steven; Gonzalez-Rodriguez, David
      Angewandte Chemie, International Edition (2016), 55 (2), 659-663CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      We present an approach that makes use of DNA base pairing to produce hydrogen-bonded macrocycles whose supramol. structure can be transferred from soln. to a solid substrate. A hierarchical assembly process ultimately leads to two-dimensional nanostructured porous networks that are able to host size-complementary guests.
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    47. 47
      Chamorro, R.; de Juan-Fernández, L.; Nieto-Ortega, B.; Mayoral, M. J.; Casado, S.; Ruiz-González, L.; Pérez, E. M.; González-Rodríguez, D. Reversible dispersion and release of carbon nanotubes via cooperative clamping interactions with hydrogen-bonded nanorings. Chem. Sci. 2018, 9, 4176– 4184,  DOI: 10.1039/C8SC00843D
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      Reversible dispersion and release of carbon nanotubes via cooperative clamping interactions with hydrogen-bonded nanorings
      Chamorro, Raquel; de Juan-Fernandez, Leire; Nieto-Ortega, Belen; Mayoral, Maria J.; Casado, Santiago; Ruiz-Gonzalez, Luisa; Perez, Emilio M.; Gonzalez-Rodriguez, David
      Chemical Science (2018), 9 (17), 4176-4184CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
      Due to their outstanding electronic and mech. properties, single-walled carbon nanotubes (SWCNTs) are promising nanomaterials for the future generation of optoelectronic devices and composites. However, their scarce soly. limits their application in many technologies that demand soln.-processing of high-purity SWCNT samples. Although some non-covalent functionalization approaches have demonstrated their utility in extg. 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 assoc. intimately with SWCNTs by embracing the tube sidewalls, which allows for an efficient SWCNT debundling and for the prodn. of long-lasting SWCNT dispersions of high optical quality along a broad concn. 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.
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    48. 48
      Garcia, F.; Korevaar, P. A.; Verlee, A.; Meijer, E. W.; Palmans, A. R. A.; Sanchez, L. The influence of [small pi]-conjugated moieties on the thermodynamics of cooperatively self-assembling tricarboxamides. Chem. Commun. 2013, 49, 8674– 8676,  DOI: 10.1039/c3cc43845g
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      The influence of π-conjugated moieties on the thermodynamics of cooperatively self-assembling tricarboxamides
      Garcia, Fatima; Korevaar, Peter A.; Verlee, Arno; Meijer, E. W.; Palmans, Anja R. A.; Sanchez, Luis
      Chemical Communications (Cambridge, United Kingdom) (2013), 49 (77), v8674-8676CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
      A detailed investigation of the self-assembly behavior of C3-sym. tricarboxamides reveals that a larger π-conjugated core does not increase the stability of assemblies in an apolar solvent but makes the system more sensitive to destabilization by addn. of a good solvent.
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    49. 49
      Chan, A. K.-W.; Wong, K. M.-C.; Yam, V. W.-W. Supramolecular Assembly of Isocyanorhodium(I) Complexes: An Interplay of Rhodium(I)···Rhodium(I) Interactions, Hydrophobic–Hydrophobic Interactions, and Host–Guest Chemistry. J. Am. Chem. Soc. 2015, 137, 6920– 6931,  DOI: 10.1021/jacs.5b03396
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      Supramolecular Assembly of Isocyanorhodium(I) Complexes: An Interplay of Rhodium(I)···Rhodium(I) Interactions, Hydrophobic-Hydrophobic Interactions, and Host-Guest Chemistry
      Chan, Alan Kwun-Wa; Wong, Keith Man-Chung; Yam, Vivian Wing-Wah
      Journal of the American Chemical Society (2015), 137 (21), 6920-6931CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Tetrakis(isocyano)rhodium(I) complexes with different chain lengths of alkyl substituents were found to exhibit a strong tendency toward soln. state aggregation upon altering the concn., temp. and solvent compn. Temp.- and solvent-dependent UV-visible absorption studies were performed, and the data were analyzed using the aggregation model to elucidate the growth mechanism. The aggregation is found to involve extensive Rh(I)···Rh(I) interactions that are synergistically assisted by hydrophobic-hydrophobic interactions to give a rainbow array of soln. aggregate colors. The presence of three long alkyl substituents is crucial for the obsd. cooperativity in the aggregation. Mol. assemblies as nanoplates and nanovesicles were obsd. in the hexane-dichloromethane solvent mixts., arising from the different formation mechanisms based on the alkyl chain length of the complexes. Benzo-15-crown-5 moieties were incorporated for selective potassium ion binding to induce dimer formation and drastic color changes, rendering the system as potential colorimetric and luminescent cation sensors and as building blocks for ion-controlled supramol. assembly.
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      Valera, J. S.; Gómez, R.; Sánchez, L. Supramolecular Polymerization of [5]Helicenes. Consequences of Self-Assembly on Configurational Stability. Org. Lett. 2018, 20, 2020– 2023,  DOI: 10.1021/acs.orglett.8b00565
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      Supramolecular Polymerization of [5]Helicenes. Consequences of Self-Assembly on Configurational Stability
      Valera, Jorge S.; Gomez, Rafael; Sanchez, Luis
      Organic Letters (2018), 20 (7), 2020-2023CODEN: ORLEF7; ISSN:1523-7052. (American Chemical Society)
      The supramol. polymn. of [5]helicenes I (1) and II (2) is investigated. The self-assembly of these helicenes proceeds by the operation of H-bonding interactions with a negligible participation of π-stacking. The enantiopurity of the sample has a dramatic effect on the supramol. polymn. mechanism since it reverts the isodesmic mechanism for the racemic mixt. to a cooperative one for the enantioenriched sample. Noticeably, the formation of supramol. polymers efficiently increases the configurational stability of 1,14-unsubstituted [5]helicenes.
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      Mayoral, M. J.; Guilleme, J.; Calbo, J.; Arago, J.; Aparicio, F.; Orti, E.; Torres, T.; Gonzalez-Rodriguez, D. Dual-Mode Chiral Self-Assembly of Cone-Shaped Subphthalocyanine Aromatics. J. Am. Chem. Soc. 2020, 142, 21017– 21031,  DOI: 10.1021/jacs.0c07291
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      Dual-Mode Chiral Self-Assembly of Cone-Shaped Subphthalocyanine Aromatics
      Mayoral, Maria J.; Guilleme, Julia; Calbo, Joaquin; Arago, Juan; Aparicio, Fatima; Orti, Enrique; Torres, Tomas; Gonzalez-Rodriguez, David
      Journal of the American Chemical Society (2020), 142 (50), 21017-21031CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Columnar polymers and liq. crystals obtained from π-conjugated cone-shaped mols. 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 mols. in soln. remains largely unexplored. Here, we show how a mol. geometry change, from flat to conic, can generate supramol. landscapes where different self-assembled species, each of them being under thermodn. equil. with the monomer, exist exclusively within distinct regimes. In particular, depending on the solvent nature - arom. or aliph. - cone-shaped C3-sym. subphthalocyanine 1 can undergo self-assembly either as a tail-to-tail dimer, showing monomer-dimer sigmoidal transitions, or as a head-to-tail noncentrosym. columnar polymer, exhibiting a nucleation-elongation polymn. mechanism. Moreover, the exptl. and theor. 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 assoc. with itself, but socially self-sort in the polymer regime, favoring an alternate stacking order along the columns.
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      Helmers, I.; Ghosh, G.; Albuquerque, R. Q.; Fernández, G. Pathway and Length Control of Supramolecular Polymers in Aqueous Media via a Hydrogen Bonding Lock. Angew. Chem., Int. Ed. 2021, 60, 4368– 4376,  DOI: 10.1002/anie.202012710
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      Pathway and Length Control of Supramolecular Polymers in Aqueous Media via a Hydrogen Bonding Lock
      Helmers, Ingo; Ghosh, Goutam; Albuquerque, Rodrigo Q.; Fernandez, Gustavo
      Angewandte Chemie, International Edition (2021), 60 (8), 4368-4376CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Programming the organization of π-conjugated systems into nanostructures of defined dimensions is a requirement for the prepn. of functional materials. Herein, we have achieved high-precision control over the self-assembly pathways and fiber length of an amphiphilic BODIPY dye in aq. media by exploiting a programmable hydrogen bonding lock. The presence of a (2-hydroxyethyl)amide group in the target BODIPY enables different types of intra- vs. intermol. hydrogen bonding, leading to a competition between kinetically controlled discoidal H-type aggregates and thermodynamically controlled 1D J-type fibers in water. The high stability of the kinetic state, which is dominated by the hydrophobic effect, is reflected in the slow transformation to the thermodn. product (several weeks at room temp.). However, this lag time can be suppressed by the addn. of seeds from the thermodn. species, enabling us to obtain supramol. polymers of tuneable length in water for multiple cycles.
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      Wu, A.; Isaacs, L. Self-Sorting: The Exception or the Rule?. J. Am. Chem. Soc. 2003, 125, 4831– 4835,  DOI: 10.1021/ja028913b
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      Self-Sorting: The Exception or the Rule?
      Wu, Anxin; Isaacs, Lyle
      Journal of the American Chemical Society (2003), 125 (16), 4831-4835CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      In this paper, we pose the question of whether self-sorting in designed systems is exceptional behavior or whether it is likely to become a more general phenomenon governing mol. recognition and self-assembly. To address this question we prepd. a mixt. comprising two of Davis' self-assembled ionophores, Rebek's tennis ball and calixarene tetraurea capsule, Meijer's ureidopyrimidinone, Reinhoudt's calixarene bis(rosette), and two mol. clips in CDCl3 soln. and obsd. the behavior of this ensemble by 1H NMR. As hypothesized, high-fidelity self-sorting behavior was obsd. The influence of several key variables - temp., concn., equil. consts., and the presence of competitors - on the fidelity of self-sorting is described. These results show that self-sorting is neither the exception nor the rule. They suggest, however, that the subset of known mol. aggregates that exceed the criteria required for thermodn. self-sorting is larger than previously appreciated and potentially quite broad.
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      Safont-Sempere, M. M.; Fernández, G.; Würthner, F. Self-Sorting Phenomena in Complex Supramolecular Systems. Chem. Rev. 2011, 111, 5784– 5814,  DOI: 10.1021/cr100357h
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      Self-Sorting Phenomena in Complex Supramolecular Systems
      Safont-Sempere, Marina M.; Fernandez, Gustavo; Wurthner, Frank
      Chemical Reviews (Washington, DC, United States) (2011), 111 (9), 5784-5814CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      A review. In this review, the authors discuss the external variables and intrinsic factors (mol. codes) that influence the recognition or discrimination of supramolecularly interacting chem. species in soln. The comprehension of this "mol. programing" in artificial systems will define the variables that control self-sorting processes, and may ultimately contribute to a better understanding of the self-assembly pathways in natural systems.
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      Aratsu, K.; Prabhu, D. D.; Iwawaki, H.; Lin, X.; Yamauchi, M.; Karatsu, T.; Yagai, S. Self-sorting regioisomers through the hierarchical organization of hydrogen-bonded rosettes. Chem. Commun. 2016, 52, 8211– 8214,  DOI: 10.1039/C6CC03419E
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      Self-sorting regioisomers through the hierarchical organization of hydrogen-bonded rosettes
      Aratsu, Keisuke; Prabhu, Deepak D.; Iwawaki, Hidetaka; Lin, Xu; Yamauchi, Mitsuaki; Karatsu, Takashi; Yagai, Shiki
      Chemical Communications (Cambridge, United Kingdom) (2016), 52 (53), 8211-8214CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)
      The self-assembly of two regioisomeric hydrogen-bonding naphthalenes was studied in mixed states in different polarity solvents. The regioisomers co-assemble to form heteromeric rosettes in chloroform. Upon injecting this soln. into methylcyclohexane the heteromeric rosettes kinetically form amorphous aggregates, which over time differentiate into thermodynamically stable distinct nanostructures through self-sorting.
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    56. 56
      Kitamoto, Y.; Pan, Z.; Prabhu, D. D.; Isobe, A.; Ohba, T.; Shimizu, N.; Takagi, H.; Haruki, R.; Adachi, S.-i.; Yagai, S. One-shot preparation of topologically chimeric nanofibers via a gradient supramolecular copolymerization. Nat. Commun. 2019, 10, 4578  DOI: 10.1038/s41467-019-12654-z
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      One-shot preparation of topologically chimeric nanofibers via a gradient supramolecular copolymerization
      Kitamoto Yuichi; Yagai Shiki; Pan Ziyan; Prabhu Deepak D; Isobe Atsushi; Yagai Shiki; Ohba Tomonori; Shimizu Nobutaka; Takagi Hideaki; Haruki Rie; Adachi Shin-Ichi
      Nature communications (2019), 10 (1), 4578 ISSN:.
      Supramolecular polymers have emerged in the last decade as highly accessible polymeric nanomaterials. An important step toward finely designed nanomaterials with versatile functions, such as those of natural proteins, is intricate topological control over their main chains. Herein, we report the facile one-shot preparation of supramolecular copolymers involving segregated secondary structures. By cooling non-polar solutions containing two monomers that individually afford helically folded and linearly extended secondary structures, we obtain unique nanofibers with coexisting distinct secondary structures. A spectroscopic analysis of the formation process of such topologically chimeric fibers reveals that the monomer composition varies gradually during the polymerization due to the formation of heteromeric hydrogen-bonded intermediates. We further demonstrate the folding of these chimeric fibers by light-induced deformation of the linearly extended segments.
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    57. 57
      Takahashi, S.; Yagai, S. Harmonizing Topological Features of Self-Assembled Fibers by Rosette-Mediated Random Supramolecular Copolymerization and Self-Sorting of Monomers by Photo-Cross-Linking. J. Am. Chem. Soc. 2022, 144, 13374– 13383,  DOI: 10.1021/jacs.2c05484
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      57
      Harmonizing Topological Features of Self-Assembled Fibers by Rosette-Mediated Random Supramolecular Copolymerization and Self-Sorting of Monomers by Photo-Cross-Linking
      Takahashi, Sho; Yagai, Shiki
      Journal of the American Chemical Society (2022), 144 (29), 13374-13383CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Random copolymn. is an effective approach to synthesize the desired polymers by harmonizing distinct properties of different monomers. For supramol. polymers in which monomer binding is inherently dynamic, it is difficult to achieve random copolymn. of monomers with distinct mol. structures and properties due to an enthalpic advantage upon self-recognition (self-sorting). Herein, we demonstrate an example of thermodynamically controlled random supramol. copolymn. of two monomers functionalized with barbituric acid via the formation of six-membered hydrogen-bonded rosette intermediates to exhibit structural harmonization of the two main-chain motifs, i.e., intrinsically curved and linear motifs. One monomer based on naphthalene chromophore exclusively forms toroidal fibers, whereas another one bearing addnl. photoreactive diacetylene moiety affords linearly elongated fibers. Supramol. copolymn. of the two monomers is achieved by cooling hot monomer mixts. in a nonpolar solvent, which results in the formation of thermodynamically stable spirally folded yet elongated fibers. Atomic force microscopic observations and theor. simulations of the exptl. data obtained by absorption spectroscopy reveal the homopolymn. of the diacetylene-functionalized monomer in the high-temp. region, followed by the incorporation of the naphthalene monomer in the medium-temp. region to form supramol. copolymers with random monomer sequence. Finally, we demonstrate that the random copolymn. process can be switched to a narcissistically self-sorting one by deactivating monomer exchange through the photo-crosslinking of the diacetylene-functionalized monomers.
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      Kang, J.; Miyajima, D.; Mori, T.; Inoue, Y.; Itoh, Y.; Aida, T. A rational strategy for the realization of chain-growth supramolecular polymerization. Science 2015, 347, 646– 651,  DOI: 10.1126/science.aaa4249
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      A rational strategy for the realization of chain-growth supramolecular polymerization
      Kang, Jiheong; Miyajima, Daigo; Mori, Tadashi; Inoue, Yoshihisa; Itoh, Yoshimitsu; Aida, Takuzo
      Science (Washington, DC, United States) (2015), 347 (6222), 646-651CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      Over the past decade, major progress in supramol. polymn. has had a substantial effect on the design of functional soft materials. However, despite recent advances, most studies are still based on a preconceived notion that supramol. polymn. follows a step-growth mechanism, which precludes control over chain length, sequence, and stereochem. structure. Here we report the realization of chain-growth polymn. by designing metastable monomers with a shape-promoted intramol. hydrogen-bonding network. The monomers are conformationally restricted from spontaneous polymn. at ambient temps. but begin to polymerize with characteristics typical of a living mechanism upon mixing with tailored initiators. The chain growth occurs stereoselectively and therefore enables optical resoln. of a racemic monomer.
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      Haedler, A. T.; Meskers, S. C. J.; Zha, R. H.; Kivala, M.; Schmidt, H.-W.; Meijer, E. W. Pathway Complexity in the Enantioselective Self-Assembly of Functional Carbonyl-Bridged Triarylamine Trisamides. J. Am. Chem. Soc. 2016, 138, 10539– 10545,  DOI: 10.1021/jacs.6b05184
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      Pathway Complexity in the Enantioselective Self-Assembly of Functional Carbonyl-Bridged Triarylamine Trisamides
      Haedler, Andreas T.; Meskers, Stefan C. J.; Zha, R. Helen; Kivala, Milan; Schmidt, Hans-Werner; Meijer, E. W.
      Journal of the American Chemical Society (2016), 138 (33), 10539-10545CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Functional supramol. systems like carbonyl-bridged triarylamine (CBT) trisamides are known for their long-range energy transport at room temp. Understanding the complex self-assembly processes of this system allows for control over generated structures using controlled supramol. polymn. Here, we present two novel CBT trisamides with (S)- or (R)-chiral side chains which show a two-pathway self-assembly behavior in soln. Depending on the thermal profile during the self-assembly process, two different stable states are obtained under otherwise identical conditions. A kinetically trapped state A is reached upon cooling to 7 °C, via a proposed isodesmic process. In addn., there is a thermodynamically stable state B at 7 °C that is induced by first undercooling to -5 °C, via a nucleation-elongation mechanism. In both cases, helical supramol. aggregates comprising H-aggregated CBTs are formed. Addnl., controlled supramol. polymn. was achieved by mixing the two different states (A and B) from the same enantiomer, leading to a conversion of the kinetically trapped state to the thermodynamically stable state. This process is highly enantioselective, as no conversion is obsd. if the two states consist of opposite enantiomers. We thus show the importance and opportunities emerging from understanding the pathway complexity of functional supramol. systems.
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      Zhang, W.; Jin, W.; Fukushima, T.; Mori, T.; Aida, T. Helix Sense-Selective Supramolecular Polymerization Seeded by a One-Handed Helical Polymeric Assembly. J. Am. Chem. Soc. 2015, 137, 13792– 13795,  DOI: 10.1021/jacs.5b09878
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      Helix sense-selective supramolecular polymerization seeded by a one-handed helical polymeric assembly
      Zhang, Wei; Jin, Wusong; Fukushima, Takanori; Mori, Tadashi; Aida, Takuzo
      Journal of the American Chemical Society (2015), 137 (43), 13792-13795CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Helix sense-selective supramol. polymn. was achieved using a 1-handed helical nanotubular polymeric assembly as a seed. First, bipyridine (BPY)-appended achiral hexabenzocoronene (BPYHBC) was copolymd. noncovalently with chiral BPYHBCS (or BPYHBCR) at a molar ratio of 9:1, which, via the sergeants-and-soldiers effect, afforded a P-helical (or M-helical) nanotube, which was then treated with Cu2+ to transform into structurally robust (BPY)CuNT(P) (or (BPY)CuNT(M)) with a Cu2+/BPY coordination polymer shell. Helical seeds (BPY)CuNT(P) and (BPY)CuNT(M) brought about the controlled assembly of fluorinated chiral FHBCS and FHBCR as well as achiral FHBC to yield 1-handed helical nanotubular supramol. block copolymers, in which the helical senses of the newly formed block segments were solely detd. by those of the helical seeds employed. Noteworthy, FHBCS and FHBCR alone without the helical seeds form ill-defined agglomerates. Attempted supramol. polymn. of a racemic mixt. of FHBCS and FHBCR from (BPY)CuNT(P) (or (BPY)CuNT(M)) resulted in its chiral sepn., affording P-helical (or M-helical) diastereomeric block segments composed of FHBCS and FHBCR with different thermodn. properties.
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      Sarkar, S.; Sarkar, A.; George, S. J. Stereoselective Seed-Induced Living Supramolecular Polymerization. Angew. Chem., Int. Ed. 2020, 59, 19841– 19845,  DOI: 10.1002/anie.202006248
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      Stereoselective Seed-Induced Living Supramolecular Polymerization
      Sarkar, Souvik; Sarkar, Aritra; George, Subi J.
      Angewandte Chemie, International Edition (2020), 59 (45), 19841-19845CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Stereoselective and temporally controlled supramol. polymns. are ubiquitous in nature and are desirable attributes for the design of chiral, well-defined functional materials. Kinetically controlled, living supramol. polymn. (LSP) has emerged recently for the synthesis of supramol. polymers with controlled length and narrow dispersity. On the other hand, stringent design requirements for chiral-discriminating monomers precludes the stereoselective control of the supramol. polymer structure. Herein, a synergetic stereo- and structural control of supramol. polymn. by the realization of an unprecedented stereoselective seed-induced LSP is reported. Homochiral and seeded growth is demonstrated with bischromophoric naphthalene diimide (NDI) enantiomers with a chiral binaphthyl amine core, exhibiting strong self-recognition abilities and pathway complexity.
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      Sarkar, S.; Sarkar, A.; Som, A.; Agasti, S. S.; George, S. J. Stereoselective Primary and Secondary Nucleation Events in Multicomponent Seeded Supramolecular Polymerization. J. Am. Chem. Soc. 2021, 143, 11777– 11787,  DOI: 10.1021/jacs.1c05642
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      62
      Stereoselective Primary and Secondary Nucleation Events in Multicomponent Seeded Supramolecular Polymerization
      Sarkar, Souvik; Sarkar, Aritra; Som, Arka; Agasti, Sarit S.; George, Subi J.
      Journal of the American Chemical Society (2021), 143 (30), 11777-11787CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Bioinspired, kinetically controlled seeded growth has been recently shown to provide length, dispersity, and sequence control on the primary structure of dynamic supramol. polymers. However, command over the mol. organization at all hierarchical levels for the modulation of higher order structures of supramol. polymers remains a formidable task. In this context, a surface-catalyzed secondary nucleation process, which plays an important role in the autocatalytic generation of amyloid fibrils and also during the chiral crystn. of small monomers, offers exciting possibilities for topol. control in synthetic macromol. systems by introducing secondary growth pathways compared to the usual primary nucleation-elongation process. However, mechanistic insights into the mol. determinants and driving forces for the secondary nucleation event in synthetic systems are not yet realized. Herein, we attempt to fill this dearth by showing an unprecedented mol. chirality control on the primary and secondary nucleation events in seed-induced supramol. polymn. Comprehensive kinetic expts. using in situ spectroscopic probing of the temporal changes of the monomer organization during the growth process provide a unique study to characterize the primary and secondary nucleation events in a supramol. polymn. process. Kinetic analyses along with various microscopic studies further reveal the remarkable effect of stereoselective nucleation and seeding events on the (micro)structural aspects of the resulting multicomponent supramol. polymers.
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      Arja, K.; Selegård, R.; Paloncýová, M.; Linares, M.; Lindgren, M.; Norman, P.; Aili, D.; Nilsson, K. P. R. Self-Assembly of Chiro-Optical Materials from Nonchiral Oligothiophene-Porphyrin Derivatives and Random Coil Synthetic Peptides. ChemPlusChem 2023, 88, e202200262  DOI: 10.1002/cplu.202200262
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      Self-Assembly of Chiro-Optical Materials from Nonchiral Oligothiophene-Porphyrin Derivatives and Random Coil Synthetic Peptides
      Arja, Katriann; Selegaard, Robert; Paloncyova, Marketa; Linares, Mathieu; Lindgren, Mikael; Norman, Patrick; Aili, Daniel; Nilsson, K. Peter R.
      ChemPlusChem (2023), 88 (1), e202200262CODEN: CHEMM5; ISSN:2192-6506. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Biomimetic chiral optoelectronic materials can be utilized in electronic devices, biosensors and artificial enzymes. Herein, this work reports the chiro-optical properties and architectural arrangement of optoelectronic materials generated from self-assembly of initially nonchiral oligothiophene-porphyrin derivs. and random coil synthetic peptides. The photo-phys.- and structural properties of the materials were assessed by absorption-, fluorescence- and CD spectroscopy, as well as dynamic light scattering, SEM and theor. calcns. The materials display a three-dimensional ordered helical structure and optical activity that are obsd. due to an induced chirality of the optoelectronic element upon interaction with the peptide. Both these properties are influenced by the chem. compn. of the oligothiophene-porphyrin deriv., as well as the peptide sequence. We foresee that our findings will aid in developing self-assembled optoelectronic materials with dynamic architectonical accuracies, as well as offer the possibility to generate the next generation of materials for a variety of bioelectronic applications.
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      Zhang, L.; Zhang, G.; Qu, H.; Todarwal, Y.; Wang, Y.; Norman, P.; Linares, M.; Surin, M.; Zhang, H.-J.; Lin, J.; Jiang, Y.-B. Naphthodithiophene Diimide Based Chiral π-Conjugated Nanopillar Molecules. Angew. Chem., Int. Ed. 2021, 60, 24543– 24548,  DOI: 10.1002/anie.202107893
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      Naphthodithiophene Diimide Based Chiral π-Conjugated Nanopillar Molecules
      Zhang, Li; Zhang, Guilan; Qu, Hang; Todarwal, Yogesh; Wang, Yun; Norman, Patrick; Linares, Mathieu; Surin, Mathieu; Zhang, Hui-Jun; Lin, Jianbin; Jiang, Yun-Bao
      Angewandte Chemie, International Edition (2021), 60 (46), 24543-24548CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      The synthesis, structures, and properties of [4]cyclonaphthodithiophene diimides ([4]C-NDTIs) are described. NDTIs as important n-type building blocks were catenated in the α-positions of thiophene rings via an unusual electrochem.-oxidn.-promoted macrocyclization route. The thiophene-thiophene junction in [4]C-NDTIs results in an ideal pillar shape. This interesting topol., along with appealing electronic and optical properties inherited from the NDTI units, endows the [4]C-NDTIs with both near-IR (NIR) light absorptions, strong excitonic coupling, and tight encapsulation of C60. Stable orientations of the NDTI units in the nanopillars lead to stable inherent chirality, which enables detailed CD studies on the impact of isomeric structures on π-conjugation. Remarkably, the [4]C-NDTIs maintain the strong π-π stacking abilities of NDTI units and thus adopt two-dimensional (2D) lattice arrays at the mol. level. These nanopillar mols. have great potential to mimic natural photosynthetic systems for the development of multifunctional org. materials.
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      Bäck, M.; Selegård, R.; Todarwal, Y.; Nyström, S.; Norman, P.; Linares, M.; Hammarström, P.; Lindgren, M.; Nilsson, K. P. R. Tyrosine Side-Chain Functionalities at Distinct Positions Determine the Chirooptical Properties and Supramolecular Structures of Pentameric Oligothiophenes. ChemistryOpen 2020, 9, 1100– 1108,  DOI: 10.1002/open.202000144
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      Tyrosine Side-Chain Functionalities at Distinct Positions Determine the Chirooptical Properties and Supramolecular Structures of Pentameric Oligothiophenes
      Back Marcus; Nystrom Sofie; Hammarstrom Per; Lindgren Mikael; Nilsson K Peter R; Selegard Robert; Todarwal Yogesh; Norman Patrick; Linares Mathieu; Linares Mathieu; Linares Mathieu; Lindgren Mikael
      ChemistryOpen (2020), 9 (11), 1100-1108 ISSN:2191-1363.
      Control over the photophysical properties and molecular organization of π-conjugated oligothiophenes is essential to their use in organic electronics. Herein we synthesized and characterized a variety of anionic pentameric oligothiophenes with different substitution patterns of L- or D-tyrosine at distinct positions along the thiophene backbone. Spectroscopic, microscopic, and theoretical studies of L- or D-tyrosine substituted pentameric oligothiophene conjugates revealed the formation of optically active π-stacked self-assembled aggregates under acid conditions. The distinct photophysical characteristics, as well as the supramolecular structures of the assemblies, were highly influenced by the positioning of the L- or D-tyrosine moieties along the thiophene backbone. Overall, the obtained results clearly demonstrate how fundamental changes in the position of the enantiomeric side-chain functionalities greatly affect the optical properties as well as the architecture of the self-assembled supramolecular structures.
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      Linares, M.; Sun, H.; Biler, M.; Andréasson, J.; Norman, P. Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra. Phys. Chem. Chem. Phys. 2019, 21, 3637– 3643,  DOI: 10.1039/C8CP05326J
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      Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra
      Linares, Mathieu; Sun, Haofan; Biler, Michal; Andreasson, Joakim; Norman, Patrick
      Physical Chemistry Chemical Physics (2019), 21 (7), 3637-3643CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
      DNA binding modes of the stereoisomeric rotamers of two dithienylethene derivs. (DTE1 and DTE2) representing candidate mol. photoswitches of great promise for photopharmacol. and nanotechnol. have been identified and characterized in terms of their binding energies and electronic CD responses. In the open form, two binding modes are identified namely minor-groove binding of the lowest-energy conformer with an anti-parallel arrangement of Me groups and major-groove double-intercalation of the P-enantiomers of an intermediate-state rotamer. Only the latter binding mode is found to be enantiomerically selective and expected to have an overall neg. linear dichroism (LD) as obsd. in the expt. for DTE1 (Angew. Chem., Int. Ed.,2013, 52, 4393). In the closed form, the most favorable binding mode is found to be minor groove binding. Also this binding mode is found to be enantiomerically selective and for DTE1, it is the M-enantiomer that binds the strongest, showing a pos. theor. signature CD band in the long wavelength region with origin in pyridinium ligands. The theor. CD spectrum is found to be in good agreement with the exptl. one, which provides an indirect evidence for a correct identification of the binding mode in the closed form.
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      Selegård, R.; Rouhbakhsh, Z.; Shirani, H.; Johansson, L. B. G.; Norman, P.; Linares, M.; Aili, D.; Nilsson, K. P. R. Distinct Electrostatic Interactions Govern the Chiro-Optical Properties and Architectural Arrangement of Peptide–Oligothiophene Hybrid Materials. Macromolecules 2017, 50, 7102– 7110,  DOI: 10.1021/acs.macromol.7b01855
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      Holmgaard List, N.; Knoops, J.; Rubio-Magnieto, J.; Idé, J.; Beljonne, D.; Norman, P.; Surin, M.; Linares, M. Origin of DNA-Induced Circular Dichroism in a Minor-Groove Binder. J. Am. Chem. Soc. 2017, 139, 14947– 14953,  DOI: 10.1021/jacs.7b05994
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      Origin of DNA-Induced Circular Dichroism in a Minor-Groove Binder
      Holmgaard List, Nanna; Knoops, Jeremie; Rubio-Magnieto, Jenifer; Ide, Julien; Beljonne, David; Norman, Patrick; Surin, Mathieu; Linares, Mathieu
      Journal of the American Chemical Society (2017), 139 (42), 14947-14953CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Induced CD (ICD) of DNA-binding ligands is well known to be strongly influenced by the specific mode of binding, but the relative importance of the possible mechanisms has remained undetd. Here, with a combination of mol. dynamics simulations, CD response calcns., and expts. on an AT-sequence, we show that the ICD of minor-groove bound DAPI (4',6-diamidino-2-phenylindole) originates from an intricate interplay between the chiral imprint of DNA, off-resonant excitonic coupling to nucleobases, charge-transfer, and resonant excitonic coupling between DAPIs. The significant contributions from charge-transfer and the chiral imprint to the ICD demonstrated the inadequacy of a std. Frenkel exciton theory of the DAPI-DNA interactions.
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      Sun, H.; Hunter, C. A.; Navarro, C.; Turega, S. Relationship between Chemical Structure and Supramolecular Effective Molarity for Formation of Intramolecular H-Bonds. J. Am. Chem. Soc. 2013, 135, 13129– 13141,  DOI: 10.1021/ja406235d
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      Relationship between Chemical Structure and Supramolecular Effective Molarity for Formation of Intramolecular H-Bonds
      Sun, Hongmei; Hunter, Christopher A.; Navarro, Cristina; Turega, Simon
      Journal of the American Chemical Society (2013), 135 (35), 13129-13141CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Effective molarity (EM) is a key parameter that dets. the efficiency of a range of supramol. phenomena from the folding of macromols. to multivalent ligand binding. Coordination complexes formed between zinc porphyrins equipped H-bond donor sites and pyridine ligands equipped with H-bond acceptor sites have allowed systematic quantification of EM values for the formation of intramol. H-bonds in 240 different systems. The results provide insights into the relationship of EM to supramol. architecture, H-bond strength, and solvent. Previous studies on ligands equipped with phosphonate diester and ether H-bond acceptors were inconclusive, but the expts. described here on ligands equipped with phosphine oxide, amide, and ester H-bond acceptors resolve these ambiguities. Chem. double-mutant cycles were used to dissect the thermodn. contributions of individual H-bond interactions to the overall stabilities of the complexes and hence det. the values of EM, which fall in the range 1-1000 mM. Solvent has little effect on EM, and the values measured in toluene and 1,1,2,2-tetrachloroethane are similar. For H-bond acceptors that have similar geometries but different H-bond strengths (amide and ester), the values of EM are very similar. For H-bond acceptors that have different geometries but similar H-bond strengths (amide and phosphonate diester), there is little correlation between the values of EM. These results imply that supramol. EMs are independent of solvent and intrinsic H-bond strength but depend on supramol. architecture and geometric complementarity.
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    • Experimental procedures and compound characterization data, along with the supramolecular study by 1H NMR, supramolecular study by optical spectroscopy, microscopy characterization of the self-assembled nanotubes, self-sorting experiments, and theoretical calculations (Figures S1–S5) (PDF)


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