The helix‐inversion mechanism in double‐stranded helical oligomers bridged by rotary cyclic boronate esters
| Autor: | Ka Hung Lee, Hiroki Iida, Taku Hayashi, Yuh Hijikata, Stephan Irle, Eiji Yashima |
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| Rok vydání: | 2019 |
| Předmět: |
010304 chemical physics
Trimethylsilyl General Chemistry 010402 general chemistry 01 natural sciences Oligomer Inversion (discrete mathematics) 0104 chemical sciences Computational Mathematics chemistry.chemical_compound Molecular dynamics Crystallography chemistry Covalent bond 0103 physical sciences Helix Molecule Potential of mean force |
| Zdroj: | Journal of Computational Chemistry. 40:2036-2042 |
| ISSN: | 1096-987X 0192-8651 |
| DOI: | 10.1002/jcc.25856 |
| Popis: | Attracted by the numerous regulatory functions of double-helical biopolymers such as DNA, many researchers have synthesized various double-helical systems. A recently synthesized double-stranded helical oligomer covalently bridged by rotary boronate esters (BBDD) was shown to undergo helix-inversion that might serve as platform to design rotor systems. However, the detailed helix-inversion mechanism could not be investigated experimentally. Direct molecular dynamics simulations based on density-functional tight-binding energies and gradients computed on-the-fly reveal that disentanglement to the unraveled form and following exchange of the twisted terminal trimethylsilyl (TMS) groups are prerequisites for the observed helix-inversion. The potential of mean force confirms that the originally assumed "concurrent" rotation of the boronate esters and the helix-inversion involves shorter time scale "step-wise" processes, triggered by the disentanglement and exchange of the TMS groups. These results indicate that inversion dynamics of double-helical molecules such as BBDD may be controllable by chemical fine-tuning of the terminal groups. © 2019 Wiley Periodicals, Inc. |
| Databáze: | OpenAIRE |
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