The
formation of purine and pyrimidine base pairs (BPs), which
contributes to shaping of the canonical and noncanonical 3D structures
of nucleic acids, is one the most investigated phenomena in chemistry
and life sciences. In this contribution, the anatomy of the bond energy
(BDE) of the base-pairing interaction in 39 different arrangements
found experimentally or predicted for DNA structures containing the
four common nucleobases (A, C, G, T) in their neutral or protonated
forms is described in light of the theory of interacting quantum atoms
within the context of the quantum theory of atoms in molecules. The
interplay of individual energy components involved in the three stages
of the bond formation process (structural deformation, electron-density
promotion, and intermolecular interaction) is studied. We recognized
that for the neutral BPs, variations in the kinetic and electrostatic
contributions to the BDE are rather negligible, leaving the exchange–correlation
energy as the main stabilizing component. It is shown that the contribution
of the exchange–correlation term can be recovered by including
atoms that are formally assumed to be hydrogen bonded (primary interaction).
In contrast, to recover the electrostatic component of interaction,
one must consider both the primary and secondary (formally nonbonded
atoms) interatomic interactions. The results of our study were employed
to design new types of BPs with altered bonding anatomy. We demonstrate
that improving the electrostatic characteristics of the BPs does not
necessarily result in greater interaction energies if weak secondary
hydrogen bonding is destroyed. However, the main tuning factor for
systems with conserved interacting faces (primary interactions) is
the electrostatic component of the interaction energy resulting from
the secondary atom–atom electrostatics.
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