Reversible Double‐Helix–Random‐Coil Transition Process of Bis{hexa(ethynylhelicene)}s
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Abstract:
Two compounds with two hexa(ethynylhelicene) parts connected by a flexible hexadecamethylene and a rigid butadiyne linker were synthesized. The 1H NMR spectroscopic and CD analyses and vapor-pressure osmometry (VPO) of these two compounds revealed intramolecular double-helix formation. Upon heating a 5-microM solution in toluene, the double-helix structure unfolded to form a random coil, and on cooling it folded again into a double helix. The thermodynamic stabilities of both structures were dependent on temperature, and the structural change in both compounds is due to the large enthalpies and entropies under equilibrium. The rate constants of their unfolding were obtained by assuming a pseudo-first-order reaction; the compound with a rigid linker unfolded slower than that with a flexible linker. The former has a larger activation energy, and its double-helix and random-coil conformers were separated by chromatography. The rate of folding was also faster for the flexible-linker compound with larger activation energy. The rate constants for the folding of both compounds slightly decreased with increasing temperature, which was ascribed to the presence of exothermic pre-equilibrium and rate-determining steps. The folding was markedly accelerated with increasing random-coil concentration, which suggests the involvement of self-catalysis. A mechanism of folding was proposed. The involvement of different mechanisms of folding and unfolding was suggested by the kinetic studies, and it was confirmed by the presence of hysteresis in the melting profiles. The difference in linker structure also affected the thermal-switching profiles of the double-helix-random-coil structural changes.Keywords:
Helix (gastropod)
Folding (DSP implementation)
Linker
Random coil
Exothermic reaction
Foldamer
Conformational isomerism
Conformational isomerism
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Nature's oligomeric macromolecules have been a long-standing source of inspiration for chemists producing foldamers. Natural systems are frequently conformationally stabilised by macrocyclisation, yet this approach has been rarely adopted in the field of foldamer chemistry. Here we present a new class of chiral cyclic trimers and tetramers formed by macrocyclisation of open-chain foldamer precursors. Symmetrical products are obtained via a [2 + 2] self-assembly approach, while full sequence control is demonstrated through linear synthesis and cyclisation of an unsymmetrical trimer. Structural characterisation is achieved through a combined X-ray and DFT approach, which indicates the tetramers adopt a near-planar conformation, while the trimers adopt a shallow bowl-like shape. Finally, a proof-of-concept experiment is conducted to demonstrate the macrocycles' capacity for cation binding.
Foldamer
Trimer
Sequence (biology)
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Conformational isomerism
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Studies on the conformational equilibria of 2-methoxy, 2-methylthio, and 2-methylselenocyclohexanol are reported. Dynamic NMR spectroscopy experiments at 203-210 K were performed, which provided the percentages of each conformer in equilibrium. Theoretical calculations using the B3LYP method and aug-cc-pvdz basis set were applied to determine the differences in energy between the conformers. The analysis of the potential energy surface of each conformer showed the presence of two rotamers. Natural bond orbital analysis provided an explanation of which factors are driving the rotamer and conformer preferences.
Conformational isomerism
Potential energy surface
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Abstract Stereoelectronic hyperconjugative interactions and the relative energies of conformers and transition states of 2‐, 3‐, and 4‐silathiacyclohexane were calculated at the B3LYP/6–311+G(d,p) level of theory. The chair conformer of 2‐silathiacyclohexane is 15.4 and 15.9 kcal mol −1 (1 kcal = 4.184 kJ), respectively, lower in energy than the chair conformers of 3‐ and 4‐silathiacyclohexane. Intrinsic reaction path calculations were used to connect the transition states between the respective chair and twist conformers and different chair–chair conformational interconversion paths were located for 3‐ and 4‐silathiacyclohexane. The energy of the transition state that connects the chair and 2,5‐twist conformers of 3‐silathiacyclohexane is 5.58 kcal mol −1 higher in energy than the chair. The transition state that connects the chair and 2,5‐twist conformers of 4‐silathiacyclohexane is 4.82 kcal mol −1 higher in energy than the chair. The energy differences (Δ E , kcal mol −1 ) between the chair conformer of 2‐silathiacyclohexane and the respective 1,4‐twist (Δ E = 4.16), 2,5‐twist (Δ E = 3.20) and 3,6‐twist (Δ E = 3.87) conformers were calculated. Small relative energy differences were calculated between the chair conformer and the respective 1,4‐twist (Δ E = 3.95), 2,5‐twist (Δ E = 4.07) and 3,6‐twist (Δ E = 3.46) conformers of 3‐silathiacyclohexane. The calculated energy differences (Δ E ) between the chair conformer and the 1,4‐twist and 2,5‐twist conformers of 4‐silathiacyclohexane were 3.50 and 4.04 kcal mol −1 , respectively. The geometric parameters and stereoelectronic hyperconjugative interactions in the silathiacyclohexanes are compared and discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Conformational isomerism
Transition state
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This note describes the design, synthesis, and conformational studies of a novel hybrid foldamer that adopts a definite compact, three-dimensional structure determined by a combined effect of the special conformational properties of the foldamer constituents. The striking feature of this de novo designed foldamer is its ability to display periodic γ-turn conformations stabilized by intramolecular hydrogen bonds. Conformational investigations by single-crystal X-ray studies, solution-state NMR, and ab initio MO theory at the HF/6-31G* level strongly support the prevalence of γ-turn motifs in both the di- and tetrapeptide foldamers, which are presumably stabilized by bifurcated hydrogen bonds in the solid and solution states. The strategy disclosed herein for the construction of hybrid foldamers with periodic γ-turn motifs has the potential to significantly augment the conformational space available for foldamer design with diverse backbone structures and conformations.
Foldamer
Tetrapeptide
Turn (biochemistry)
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Conformational isomerism
Isobar
Supercritical Carbon Dioxide
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This chapter discusses efforts along those lines and achievements in the formation of foldamer-based nanostructures in the aqueous environment. Helical foldamers are good candidates to build such artificial helix bundles. Mainly two approaches have been reported in the literature: a "top-down" approach, in which a natural peptide sequence known to form coiled coil structures is used as a starting scaffold to construct a nonnatural hybrid foldamer/peptide sequence that self-associates into bundles, or a "bottom-up" approach, in which the self-assembly is based on de novo designed amphiphilic foldamer helices with segregation of hydrophilic and lipophilic side chains. Several foldamer backbones were shown to render accessible elongated supramolecular nanostructures such as fibers, filament, and tubes akin to those formed by proteins and peptides. The chapter suggests the enticing opportunities for the creation of metal-coordinated nanostructures using appropriate oligomer sequences as foldable strands.
Foldamer
Sequence (biology)
Helix (gastropod)
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