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. 2019 Nov 28;48(2):924–933. doi: 10.1093/nar/gkz1096

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — RNA MD simulations and DFT calculations. (A) Simulation system with two molecules (red) incorporated in the RNA helix (lime), solvated in a periodic truncated octahedral box of water (blue) with Na⁺ (yellow) and Cl⁻ ions (green). (B) Structure of the molecule corresponding to a dihedral angle d1 of 0° (syn). (C) DFT relaxed surface scans of the dihedral angle d1 in the molecule at B3LYP-GD3BJ/cc-pVTZ and PBE0/N07D levels of theory. Energies are relative to the minimum energy structure of each scan.

Inline graphic — RNA MD simulations and DFT calculations. (A) Simulation system with two molecules (red) incorporated in the RNA helix (lime), solvated in a periodic truncated octahedral box of water (blue) with Na⁺ (yellow) and Cl⁻ ions (green). (B) Structure of the molecule corresponding to a dihedral angle d1 of 0° (syn). (C) DFT relaxed surface scans of the dihedral angle d1 in the molecule at B3LYP-GD3BJ/cc-pVTZ and PBE0/N07D levels of theory. Energies are relative to the minimum energy structure of each scan.