The helix‐inversion mechanism in double‐stranded helical oligomers bridged by rotary cyclic boronate esters

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.

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