Issue 41, 2020

Intrinsic dynamic and static nature of each HB in the multi-HBs between nucleobase pairs and its behavior, elucidated with QTAIM dual functional analysis and QC calculations

Abstract

The intrinsic dynamic and static nature of each HB in the multi-HBs between nucleobase pairs (Nu–Nu′) is elucidated with QTAIM dual functional analysis (QTAIM-DFA). Perturbed structures generated using coordinates derived from the compliance constants (Cii) are employed for QTAIM-DFA. The method is called CIV. Two, three, or four HBs are detected for Nu–Nu′. Each HB in Nu–Nu′ is predicted to have the nature of CT-TBP (trigonal bipyramidal adduct formation through charge transfer (CT)), CT-MC (molecular complex formation through CT), or t-HBwc (typical HB with covalency), while the vdW nature is predicted for the C–H⋯X interactions, for example. Energies for the formation of the pairs (ΔE) are linearly correlated with the total values of Cii−1 in Nu–Nu′. The total Cii−1 values are obtained by summing each Cii−1 value, similarly to the case of Ohm's law for the parallel connection in the electric resistance. The total ΔE value for a nucleobase pair could be fractionalized to each HB, based on each Cii−1 value. The perturbed structures generated with CIV are very close to those generated with the partial optimization method, when the changes in the interaction distances are very small. The results provide useful insights for better understanding DNA processes, although they are highly enzymatic.

Graphical abstract: Intrinsic dynamic and static nature of each HB in the multi-HBs between nucleobase pairs and its behavior, elucidated with QTAIM dual functional analysis and QC calculations

Supplementary files

Article information

Article type
Paper
Submitted
12 Feb 2020
Accepted
22 Jun 2020
First published
01 Jul 2020
This article is Open Access
Creative Commons BY-NC license

RSC Adv., 2020,10, 24730-24742

Intrinsic dynamic and static nature of each HB in the multi-HBs between nucleobase pairs and its behavior, elucidated with QTAIM dual functional analysis and QC calculations

W. Nakanishi, S. Hayashi and T. Nishide, RSC Adv., 2020, 10, 24730 DOI: 10.1039/D0RA01357A

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