Control of Duplex Formation and Columnar Self-Assembly with Heterogeneous Amide/Urea Macrocycles

Effective self-assembly of 21- and 14-membered azamacrocycles via condition-controlled cyclotrimerization or cyclodimerization of different thiosemicarbazide-based precursors

A preparative synthesis of previously unknown 21- and 14-membered azamacrocycles via acid-promoted cyclotrimerization or cyclodimerization of three readily available precursors, namely, 1-amino-6-hydroxy-4,6-dimethylhexahydropyrimidine-2-thione, 4-(4-oxopent-2-yl)thiosemicarbazide hydrazone, and 5,7-dimethyl-1,4,5,6-tetrahydro-3H-1,2,4-triazepine-3-thione has been developed. A dramatic dependence of the selectivity of macrocyclization on the reaction conditions is demonstrated. The thermodynamic aspects of the reactions are discussed based on experimental data and DFT calculation results. Plausible pathways for the formation of macrocycles are proposed.

Pervasive approximate periodic symmetry in organic P1 structures

The goal of this project was to identify the prevalence of approximate symmetry in organic P1 structures. In the November 2019 version of the Cambridge Structural Database (CSD), there are 2592 organic, P1, R ≤ 0.050 structures; complete, unique entries are available for 1407 Z = Z' > 1 and 1049 Z = Z' = 1 structures. All the Z > 1 structures can have approximate symmetry; the Z = 1 structures were scanned to find those composed of molecules or ions that might lie on a special position and those that have two or more large molecules or ions that are very similar. The number of Z = 1 structures so identified was 285, of which 49 were grouped with the Z > 1 structures because Z_effective > 1. The packing in each of the 1407 + 285 = 1692 structures was investigated. The 144 that should almost certainly have been described in a smaller or higher-symmetry unit cell were removed from the list; 120 of the 144 are composed of achiral or racemic material. (About half of the Z = 1 and 89% of the Z > 1 structures are composed of enantiopure material.) Approximate periodic symmetry was found in 86% of the 1337 remaining Z > 1 structures and in 72% of the 211 remaining Z = 1 structures. About a third of the enantiomerically pure structures mimic inversion symmetry; 38% have approximate rotational symmetry. For the structures of achiral and racemic material, distorted glide or mirror symmetry is more common than is distorted inversion symmetry. Approximate rotational and glide symmetry was found to be periodic in two dimensions considerably more often than in three. In 4% of the structures, different layer types alternate or layers are related by approximate local rotations, as well as by small translations. In 5% of the structures, different parts of the molecule are segregated into two-dimensional regions that have different approximate symmetries. More than a third of the structures that are a distorted version of a higher-symmetry structure were determined at T ≥ 288 K.

Advances in hybrid peptide-based self-assembly systems and their applications

Self-assembly of peptides demonstrates a great potential for designing highly ordered, finely tailored supramolecular arrangements enriched with high specificity, improved efficacy and biological activity. Along with natural peptides, hybrid peptide systems composed of natural and chemically diverse unnatural amino acids have been used in various fields, including drug delivery, wound healing, potent inhibition of diseases, and prevention of biomaterial related diseases to name a few. In this review, we provide a brief outline of various methods that have been utilized for obtaining fascinating structures that create an avenue to reproduce a range of functions resulting from these folds. An overview of different self-assembled structures as well as their applications will also be provided. We believe that this review is very relevant to the current scenario and will cover conformations of hybrid peptides and resulting self-assemblies from the late 20^th century through 2022. This review aims to be a comprehensive and reliable account of the hybrid peptide-based self-assembly owing to its enormous influence in understanding and mimicking biological processes.

Chiral nanostructuring of multivalent macrocycles in solution and on surfaces

We describe the design and synthesis of a novel functionality-rich, homochiral macrocycle, possessing the overall molecular D2 symmetry, in which multivalency is introduced into the covalent framework by means of four suitably positioned pyridine moieties. The macrocycle synthesis is carried out with functionalized, enantiopure 1,1'-binaphthyl synthons as the source of chirality by means of a room temperature esterification reaction as the cyclization procedure. Upon addition of Pd(2+), coordination of the pyridine moieties occurs both intra and intermolecularly, to afford chiral ordered mono and dimeric macrocycles or multimeric aggregates depending on the solvents and conditions used. The metal binding event takes place in combination with a significant macrocyclic conformational rearrangement detected by circular dichroism spectroscopy. When in combination with a third component (C60), the macrocycle-Pd(2+) hybrid undergoes surface-confined nanostructuring into chiral nanofibres.

Design and synthesis of conformationally homogeneous pseudo cyclic peptides through amino acid insertion: investigations on their self assembly

Macrocyclic C₂ symmetric peptides have been synthesized that contain bis furanoid triazole amino acids linked to a d-α-amino acid or a β-amino acid in each half. Only the former undergoes parallel homo-stacking in solution.

Homochiral BINOL-based macrocycles with π-electron-rich, electron-withdrawing or extended spacing units as receptors for C60

The “one-pot” synthesis of several homochiral macrocycles has been achieved by using π-electron-rich, electron-deficient or extended aromatic dicarboxylic acids in combination with an axially-chiral dibenzylic alcohol, derived from enantiomerically-pure BINOL. Two series of cyclic adducts with average molecular D₂ and D₃ molecular symmetries, respectively, have been isolated in pure forms. Their yields and selectivities deviate substantially from statistical distributions. NMR and CD spectroscopic methods are efficient and functional in order to highlight the variability of shapes of the covalent macrocyclic frameworks. The larger D₃ cyclic adducts exhibit recognition properties towards C₆₀ in toluene solutions (up to log K_a = 3.2) with variable stoichiometries and variable intensities of the charge-tranfer band upon complexation.

Construction of cucurbit[7]uril based tubular nanochannels incorporating associated [CdCl4]2- and lanthanide ions

There is intensive interest in the design of tubular channels because of their novel structures and various applications in a variety of research fields. Herein, we present a series of coordination-driven Q[7]-derived organic nanochannels using an anion-induced strategy under different acid concentrations. An advantage of this approach is that the tubular channels not only retain the original character of the parent macrocyclic receptors but also provide deep hydrophobic cavities possessing guest binding sites. Importantly, this study also emphasizes the efficiency of the macrocyclic receptors in providing a tubular hydrophobic cavity by directly stacking on top of one another with the anion-fixed and by acid control. The resulting combination of hydrogen bonding, C-H···Cl, and ion-dipole interactions helps to stabilize these supramolecular architectures. Such systems are both tunable and versatile and allow for interconvertibility in the construction of nanochannels based on these macrocyclic receptors.

Synthesis and anion recognition properties of shape-persistent binaphthyl-containing chiral macrocyclic amides

We report on the synthesis and characterization of novel shape-persistent, optically active arylamide macrocycles, which can be obtained using a one-pot methodology. Resolved, axially chiral binol scaffolds, which incorporate either methoxy or acetoxy functionalities in the 2,2' positions and carboxylic functionalities in the external 3,3' positions, were used as the source of chirality. Two of these binaphthyls are joined through amidation reactions using rigid diaryl amines of differing shapes, to give homochiral tetraamidic macrocycles. The recognition properties of these supramolecular receptors have been analyzed, and the results indicate a modulation of binding affinities towards dicarboxylate anions, with a drastic change of binding mode depending on the steric and electronic features of the functional groups in the 2,2' positions.

A triple helical structure supported solely by C-H···O hydrogen bonding

A novel triple helical structure that is self-assembled by cationic molecules, 1-acetamido-3-(2-pyrazinyl)-imidazolium, is reported. The computational analysis underpins that the formation of the triple helix is driven by C-H···O hydrogen bonding.

Design, synthesis, and structural analysis of D,L-mixed polypyrrolinones. 2. Macrocyclic hexapyrrolinones

The design, synthesis, and structural analysis of two macrocyclic D,L-alternating hexapyrrolinones have been achieved. These cyclic peptide mimics adopt a flat, hexagonal conformation, stabilized by intramolecular hydrogen bonding between adjacent pyrrolinone rings. Extensive NMR studies and X-ray analysis reveal, respectively, that the macrocyclic hexapyrrolinones aggregate in solution and in the solid state form staggered stacked nanotube-like assemblies.