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

Hayashi, Taku; Lee, Ka Hung; Iida, Hiroki; Yashima, Eiji; Irle, Stephan; Hijikata, Yuh

doi:10.1002/jcc.25856

Title: The helix⁻inversion mechanism in double₋stranded helical oligomers bridged by rotary cyclic boronate esters

Journal Article · Thu May 16 00:00:00 EDT 2019 · Journal of Computational Chemistry

DOI:https://doi.org/10.1002/jcc.25856· OSTI ID:1557504

Hayashi, Taku ^[1];

^[2];

^[3];

^[1];

^[4];

^[1]

Nagoya Univ. (Japan)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Shimane Univ. (Japan)
Nagoya Univ. (Japan); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)

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. Yet, 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 possibility 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 suggest that inversion dynamics of double-helical molecules such as BBDD may be controllable by chemical fine-tuning of the terminal groups.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; Japan Society for the Promotion of Science (JSPS)

Grant/Contract Number:: AC05-00OR22725; AC05‐00OR22725

OSTI ID:: 1557504

Alternate ID(s):: OSTI ID: 1513060

Journal Information:: Journal of Computational Chemistry, Vol. 40, Issue 23; ISSN 0192-8651

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
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Title: The helix⁻inversion mechanism in double₋stranded helical oligomers bridged by rotary cyclic boronate esters

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