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:
-
- 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)
- 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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