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

Abstract

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.

Authors:
 [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [1]; ORCiD logo [4]; ORCiD logo [1]
  1. Nagoya Univ. (Japan)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  3. Shimane Univ. (Japan)
  4. Nagoya Univ. (Japan); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE; Japan Society for the Promotion of Science (JSPS)
OSTI Identifier:
1557504
Alternate Identifier(s):
OSTI ID: 1513060
Grant/Contract Number:  
AC05-00OR22725; AC05‐00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Computational Chemistry
Additional Journal Information:
Journal Volume: 40; Journal Issue: 23; Journal ID: ISSN 0192-8651
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; double‐helical structure; helix‐inversion; molecular dynamics simulation; density‐functional tight‐binding; potential of mean force

Citation Formats

Hayashi, Taku, Lee, Ka Hung, Iida, Hiroki, Yashima, Eiji, Irle, Stephan, and Hijikata, Yuh. The helix⁻inversion mechanism in double₋stranded helical oligomers bridged by rotary cyclic boronate esters. United States: N. p., 2019. Web. doi:10.1002/jcc.25856.
Hayashi, Taku, Lee, Ka Hung, Iida, Hiroki, Yashima, Eiji, Irle, Stephan, & Hijikata, Yuh. The helix⁻inversion mechanism in double₋stranded helical oligomers bridged by rotary cyclic boronate esters. United States. https://doi.org/10.1002/jcc.25856
Hayashi, Taku, Lee, Ka Hung, Iida, Hiroki, Yashima, Eiji, Irle, Stephan, and Hijikata, Yuh. Thu . "The helix⁻inversion mechanism in double₋stranded helical oligomers bridged by rotary cyclic boronate esters". United States. https://doi.org/10.1002/jcc.25856. https://www.osti.gov/servlets/purl/1557504.
@article{osti_1557504,
title = {The helix⁻inversion mechanism in double₋stranded helical oligomers bridged by rotary cyclic boronate esters},
author = {Hayashi, Taku and Lee, Ka Hung and Iida, Hiroki and Yashima, Eiji and Irle, Stephan and Hijikata, Yuh},
abstractNote = {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.},
doi = {10.1002/jcc.25856},
journal = {Journal of Computational Chemistry},
number = 23,
volume = 40,
place = {United States},
year = {Thu May 16 00:00:00 EDT 2019},
month = {Thu May 16 00:00:00 EDT 2019}
}

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