Homopairing Possibilities of the DNA Base Adenine

Abstract

Using calculations based on the ab initio density functional theory, we for the first time report all possible planar DNA base adenine homodimers. Two density functionals and both localized and plane wave basis sets were used, and the results are compared with previous quantum chemical and semiempirical calculations available for a few pairs. We find that there are 21 possible planar adenine pairs with variable binding energies ranging from -0.03 to -0.86 eV. More stable pairs are associated with two strong hydrogen bonds formed between the monomers, while the least stable pairs are characterized by two or one relatively weak bonds. We find that stable hydrogen bonds can be characterized by the difference charge density that shows well-developed regions of alternating excess and depletion of the electron charge similar to a "kebab" structure. The presented detailed information on all planar adenine pairs can be utilized, for example, in considering possible adenine monolayers seen on various surfaces.