Intermolecular hydrogen bonding delineates the stability of non-canonical adenine base pairs: a first-principles study

Abstract

Non-canonical nucleobase pairs differ from canonical Watson–Crick (WC) pairs in their hydrogen bonding patterns. This study uses density functional theory with empirical dispersion correction to examine the stability and electronic properties of free adenine dimers stabilized by hydrogen bonds along the WC, Sugar (S), and Hoogsteen (H) edges. Dispersion correction is crucial for accurate interaction energy evaluation. The most stable adenine dimer is stabilized by N–H⋯N hydrogen bonds in gas and solvent phases. Binding energy decreases by ∼10.2 kcal mol⁻¹ for dimers with both C–H⋯N and N–H⋯N bonds, increasing the donor–acceptor distance. However, with a sugar–phosphate backbone, dimers with C–H⋯N and N–H⋯N bonds have higher binding energy in an implicit solvent, emphasizing the role of C–H⋯N interactions in stability and nucleic acid folding dynamics. This study highlights noncovalent interactions, such as hydrogen bonding and π–π stacking, within adenine pairs with potential applications in biosensing and DNA-based self-assembly on nanomaterial interfaces.