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

Published on Jun 24, 2020in RSC Advances3.119
· DOI :10.1039/D0RA01357A
Waro Nakanishi25
Estimated H-index: 25
(Wakayama University),
Satoko Hayashi25
Estimated H-index: 25
(Wakayama University),
Taro Nishide2
Estimated H-index: 2
(Wakayama University)
Sources
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.
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