skip to main content

This content will become publicly available on May 26, 2022

Title: Folding-controlled assembly of ortho -phenylene-based macrocycles
The self-assembly of foldamers into macrocycles is a simple approach to non-biological higher-order structure. Previous work on the co-assembly of ortho -phenylene foldamers with rod-shaped linkers has shown that folding and self-assembly affect each other; that is, the combination leads to new emergent behavior, such as access to otherwise unfavorable folding states. To this point this relationship has been passive. Here, we demonstrate control of self-assembly by manipulating the foldamers' conformational energy surfaces. A series of o -phenylene decamers and octamers have been assembled into macrocycles using imine condensation. Product distributions were analyzed by gel-permeation chromatography and molecular geometries extracted from a combination of NMR spectroscopy and computational chemistry. The assembly of o -phenylene decamers functionalized with alkoxy groups or hydrogens gives both [2 + 2] and [3 + 3] macrocycles. The mixture results from a subtle balance of entropic and enthalpic effects in these systems: the smaller [2 + 2] macrocycles are entropically favored but require the oligomer to misfold, whereas a perfectly folded decamer fits well within the larger [3 + 3] macrocycle that is entropically disfavored. Changing the substituents to fluoro groups, however, shifts assembly quantitatively to the [3 + 3] macrocycle products, even though the structural more » changes are well-removed from the functional groups directly participating in bond formation. The electron-withdrawing groups favor folding in these systems by strengthening arene–arene stacking interactions, increasing the enthalpic penalty to misfolding. The architectural changes are substantial even though the chemical perturbation is small: analogous o -phenylene octamers do not fit within macrocycles when perfectly folded, and quantitatively misfold to give small macrocycles regardless of substitution. Taken together, these results represent both a high level of structural control in structurally complex foldamer systems and the demonstration of large-amplitude structural changes as a consequence of a small structural effects. « less
Award ID(s):
Publication Date:
Journal Name:
Chemical Science
Page Range or eLocation-ID:
6992 to 7002
Sponsoring Org:
National Science Foundation
More Like this
  1. The conversion of macrocyclic 1,4-diketones to highly strained para-phenylene rings has recently been reported by our laboratory. This synthetic strategy represents a non-cross-coupling-based approach to arene-bridged macrocycles, and an alternative to palladium- and nickel-mediated processes. In this Synpacts article we discuss the development of endgame aromatization protocols for the synthesis of increasingly strained arene systems, as well as potential advantages of the macrocyclic 1,4-diketone approach to selectively functionalized benzenoid macrocycles for future complexity building reactions. 1 Introduction 2 A Non-Cross-Coupling-Based Approach to Arene-Bridged Macro cycles 3 Macrocyclic 1,4-Diketones: Streamlined Synthesis and Size-­Dependent Diastereoselective Grignard Reactions 4 Dehydrative Aromatization Reactions: Amore »Powerful Tool for Synthesizing Highly Strained para-Phenylene Units 5 Conclusion« less
  2. We demonstrated ion-mobility spectrometry mass spectrometry (IMS-MS) as a powerful tool for interrogating and preserving selective chemistry including non-covalent and host–guest complexes of m -xylene macrocycles formed in solution. The technique readily revealed the unique favorability of a thiourea-containing macrocycle MXT to Zn 2+ to form a dimer complex with the cation in an off-axis sandwich structure having the Zn–S bonds in a tetrahedral coordination environment. Replacing thiourea with urea generates MXU which formed high-order oligomerization with weak binding interactions to neutral DMSO guests detected at every oligomer size. The self-assembly pathway observed for this macrocycle is consistent with themore »crystalline assembly. Further transformation of urea into squaramide produces MXS, a rare receptor for probing sulfate in solution. Tight complexes were observed for both monomeric and dimeric of MXS in which HSO 4 − bound stronger than SO 4 2− to the host. The position of HSO 4 − at the binding cavity is a 180° inversion of the reported crystallographic SO 4 2− . The MXS dimer formed a prism-like shape with HSO 4 − exhibiting strong contacts with the 8 amine protons of two MXS macrocycles. By eliminating intermolecular interferences, we detected the low energy structures of MXS with collisional cross section (CCS) matching cis – trans and cis – cis squaramides-amines, both were not observed in crystallization trials. The experiments collectively unravel multiple facets of macrocycle chemistry including conformational flexibility, self-assembly and ligand binding; all in one analysis. Our findings illustrate an inexpensive and widely applicable approach to investigate weak but important interactions that define the shape and binding of macrocycles.« less
  3. Carbohydrate derived low molecular weight organogelators are interesting compounds with many potential applications. Selective functionalization of the different hydroxyl substituents on d -glucose and d -glucosamine resulted in small molecular gelators. Previously we have found that the C-2 acylated derivatives including esters and carbamates of 4,6- O -benzylidene protected glucose and glucosamine derivatives have shown remarkable applications as molecular gelators. In this research, in order to probe the structural influence of sugar derivatives on molecular self-assembly, we introduced acylation functional groups to the 3-hydroxyl group of 4,6- O -benzylidene acetal protected N -acetyl glucosamine derivatives. A library of fourteen estermore »derivatives was synthesized and characterized. The ester derivatives typically formed gels in pump oil and aqueous mixtures of dimethyl sulfoxide or ethanol. The resulting gels were characterized using optical microscopy, and rheology, etc. All alkyl ester derivatives were gelators for pump oil. A short chain ester derivative was able to form gels in a few different oils and the corresponding oil water mixtures phase selectively. The compound was also used to trap naproxen sodium and formed a stable co-gel. The controlled release of the drug from the gel to the aqueous phase was analyzed using UV-vis spectroscopy. These results show that the functionalization at the 3-OH position of the N -acetyl glucosamine derivative is a feasible strategy in designing new classes of organogelators.« less
  4. Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg2+ions or by interaction with ribosomal proteins. To provide a quantitative description of ion-induced folding of the ∼350-nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg2+concentration between 0 and 30 mM. The Mg2+dependence of the radius of gyration shows that globallymore »the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg2+concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg2+ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg2+-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg2+-induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome.

    « less
  5. In this paper, we show that the rigid-foldability of a given crease pattern using all creases is weakly NP-hard by a reduction from the partition problem, and that rigid-foldability with optional creases is NP-hard by a reduction from the 1-in-3 SAT problem. Unlike flat-foldabilty of origami or flexibility of other kinematic linkages, whose complexity originates in the complexity of the layer ordering and possible self-intersection of the material, rigid foldabilltiy from a planar state is hard even though there is no potential self-intersection. In fact, the complexity comes from the combinatorial behavior of the different possible rigid folding configurations atmore »each vertex. The results underpin the fact that it is harder to fold from an unfolded sheet of paper than to unfold a folded state back to a plane, frequently encountered problem when realizing folding-based systems such as self-folding matters and reconfigurable robots.« less