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Containers and Vessels for Supramolecular Catalysis
Published in Jubaraj Bikash Baruah, Principles and Advances in Supramolecular Catalysis, 2019
Foldamers are folded structures of oligomers with specific compact conformations. The structure of foldamers varies with conditions and is guided by weak intramolecular interactions. The folded and stretched forms of such compounds may be compared to a millipede. While in motion, a millipede is in the open form; a millipede goes to a protective mode and adopts a folded form (Figure 3.16). Folded molecules with active sites in reorganised and pre-organised states are useful for catalytic reactions. For example, the poly-urea derivative 3.17a has a folded structure. This urea derivative with flexible tethers has a thiourea unit attached at one end. The folded structure has two urea sites exposed outwards from the folds, which are readily available to bind substrates to activate for catalytic reactions. Based on such a model, catalysts are developed. The foldamer 3.17a is used for enantioselective carbon—carbon bond formation. The reaction between 1-((E)-2-nitrovinyl)benzene and diethylmalonate is catalysed by a peptide to form diethyl 2-((R)-2-nitro-1-phenylethyl)malonate in 95% enantionmeric excess (Figure 3.17).
Synthesis, Structures, and Functions of Helical π-Conjugated Polymers
Published in Atsushi Nagai, Koji Takagi, Conjugated Objects, 2017
Hiromitsu Sogawa, Kazuko Nakazono, Toshikazu Takata
This section describes recent advances in foldamer-type π-conjugated polymers (Fig. 8.11). According to Gellman25, foldamers are “any polymer with a strong tendency to adopt a specific compact conformation.” Oligo(m-phenylene ethynylene) foldamers were first developed by Moore and coworkers in 1997. Optically active oligo(m- phenylene ethynylene)s bearing ethylene glycol units (26) folded into predominantly one-handed helices in polar solvents because of their amphiphilicity, which originated from their hydrophilic side chains and hydrophobic main chains (Fig. 8.11).26 The para-linked poly(phenylene ethynylene)s bearing chiral side chains exhibited strong bisignate CD signals as a result of aggregation, demonstrating that the meta connectivity of the monomer units played an important role in the oligomer folding into a helix.27 Optically active polymers with analogous main chains also adopted a helical conformation with a biased screw sense (Fig. 8.12).28 Polymer 27 exhibited strong bisignate CD signals in methanol, water, and their mixtures, consistent with the formation of folded helical structures presenting a preferred handedness.28c A poly(m-phenylene ethynylene)-based polyradical bearing galvinoxyl and chiral pinanyl pendant groups (28) showed a weak but characteristic CD in methanol/chloroform mixtures.28d Poly(m-phenylenedisilanylene) (29) comprising a ό-π-conjugated main chain exhibited positive Cotton effects in the absorption region of the main chain in methanol but no intense CD signals in CH2Cl2.
Design of artificial cells: artificial biochemical systems, their thermodynamics and kinetics properties
Published in Egyptian Journal of Basic and Applied Sciences, 2022
Adamu Yunusa Ugya, Lin Pohan, Qifeng Wang, Kamel Meguellati
While the energetics and dynamics of folding in natural proteins is well studied, little is known about the forces that govern folding in modified backbones which determines the secondary structure of the protein. The thermodynamic consequences of backbone alteration on protein folding, focusing on two types of chemical changes made in different structural contexts of a compact tertiary fold can be studied employing foldamers. Foldamers are sequence-specific oligomers similar to peptides, proteins and oligonucleotides that fold into well-defined three dimensional structures. The latest results show an increase of the folding entropy that induced by the modified cations increase disorder in the ensemble of unfolded states. This is attributed mainly due to differences in the solvation of natural and unnatural backbones [124]. Although natural proteins are made up exclusively of α-amino acids, numerous unnatural polypeptides exhibit ordered folds with interesting biological activities. The thermodynamics of the backbone is determined by the non-covalent interactions. However, the rules used in most studies have been developed with peptides and proteins composed of α amino acids, which leads to the question of whether our understanding is only valid for conventional peptides, or whether it is truly molecular in nature [125]. In natural biological systems amino acids having both the amine and the carboxylic acid groups attached to the rest (alpha-) carbon atom are almost exclusively present. New folded backbones, including hybrids of aromatic and aliphatic backbones, will lead to increasingly diverse platforms for recognition of a variety of biomolecules and surfaces. In general, replacing ɑ-residues with β3-residues is enthalpically unfavorable and entropically favorable to the thermodynamic stability of the tertiary structure [124]. A key structural difference between ɑ-residues and β3-residues are an additional rotatable bond in the backbone, which results in increased conformational flexibility. Chandramouli et al. gave a beautiful example of the design of an artificial helically folded aromatic oligoamide for the selective encapsulation of fructose [126]. The molecular recognition of saccharides by both natural and artificial receptors is seriously challenged by the issues of affinity and selectivity. Using fructose as a test case, extensive and unprecedented structural information about saccharide recognition at the atomic level was provided, shedding light on the binding mechanism of these intractable natural substrates [127].