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. 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.
| Original language | English |
|---|---|
| Pages (from-to) | 2036-2042 |
| Number of pages | 7 |
| Journal | Journal of Computational Chemistry |
| Volume | 40 |
| Issue number | 23 |
| DOIs | |
| State | Published - Sep 5 2019 |
Funding
This work is supported by the Grant-in-Aid for Specially Promoted Research (Grant Number JP18H05209). S. I. was supported in part by the Laboratory Directed Research and Development (LDRD) Program of Oak Ridge National Laboratory. ORNL is managed by UT-Battelle, LLC, for DOE under Contract DE-AC05-00OR22725. [a] T. Hayashi Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan [b] K. H. Lee Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831-6493 [c] K. H. Lee Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, 37996 [d] H. Iida Department of Chemistry, Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Japan [e] E. Yashima Department of Molecular Design and Engineering and Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8063, Japan [f] S. Irle Department of Chemistry, Graduate School of Science and Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan E-mail: [email protected] [g] S. Irle Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831-6493 [h] S. Irle Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, 37996 [i] Y. Hijikata Department of Chemistry, Graduate School of Science and Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan E-mail: [email protected] Contract Grant sponsor: Japan Society for the Promotion of Science; Contract Grant number: JP18H05209; Contract Grant sponsor: Oak Ridge National Laboratory; Contract Grant sponsor: DOE; Contract Grant number: DE-AC05-00OR22725; Contract Grant sponsor: Oak Ridge National Laboratory
| Funders | Funder number |
|---|---|
| Graduate School of Natural Science and Technology | |
| Graduate School of Science and Institute of Transformative Bio-Molecules | |
| Interdisciplinary Research and Graduate Education | |
| UT-Battelle | |
| U.S. Department of Energy | DE-AC05-00OR22725 |
| Oak Ridge National Laboratory | |
| Laboratory Directed Research and Development | |
| University of Tennessee | |
| Japan Society for the Promotion of Science | JP18H05209 |
| Shimane University | |
| Nagoya University |
Keywords
- density-functional tight-binding
- double-helical structure
- helix-inversion
- molecular dynamics simulation
- potential of mean force