Hexagonal adenine networks constructed from their homopairings

• Published in: Surface science 2005-09, Vol.589 (1), p.139-152
• Main Authors: Kelly, R.E.A., Kantorovich, L.N.
• Format: Article
• Language: English
• Subjects: Biological molecules-nucleic acids; Condensed matter: electronic structure, electrical, magnetic, and optical properties; Condensed matter: structure, mechanical and thermal properties; Cross-disciplinary physics: materials science; rheology; Exact sciences and technology; Hydrogen bonding; Organic monolayers; Physics; Self-assembly; Super-structure
• ISSN: 0039-6028; 1879-2758
• DOI: 10.1016/j.susc.2005.05.060

Employing previously reported results of ab initio calculations of all planar adenine pairs, we suggest a simple method enabling us to predict most of the possible arrangements of the DNA base adenine into hexagonal networks, i.e. super-structures with three-fold coordination of each monomer. Depending on the substrate, different self-assembled adenine monolayers have been observed experimentally, and if one can assume that there is small interaction with the substrate, all these structures should be predicted in this study. We find that thousands of energetically favourable monolayers are possible, just a few of which have been studied so far. Full relaxation density functional theory (DFT) calculations applied to a finite set of randomly selected monolayers showed a good correlation with the predicted structures and binding energies. Our method can be used for an efficient preliminary analysis of possible self-assembled super-structures of organic molecules stabilised primarily by the hydrogen bonding between the monomers.