Structures and properties of the planar G•C•G•C tetrads:: Ab initio HF and DFT studies

To reveal the details of molecular geometries and properties of the GCGC tetrad, reliable quantum chemical methods (HF and DFT) in conjunction with a large basis set (6-311G(d,p)) were used to locate the local minima of the GCGC tetrad structures-and to predict their energies and electrostatic potential maps. The study reveals that both A type forms of the GCGC tetrad form stable structures. The stabilization energies relative to the isolated bases amount to approximately 72 kcal/mol more than was predicted for the isolated G tetrad. The inter GC pair interaction contributes about 17-19 kcal/mol to the total stabilization energy. The large stabilization energies confirm that the stabilization of the tetrads plays a key role in the four-stranded helices. The GCGC-a1 conformer formed through the inter base pair H(N4)-O6 hydrogen bonding is about 2 kcal/mol more stable than the GCGC-a2 form. However, the relative stability of both forms could be affected by the presence of cations that might balance the electrostatic repulsion of the O6-O6' atomic pair in the tetrad. The study also reveals the importance of the cooperative effect of hydrogen bonding in the formation of GCGC tetrads. The presence of the inter base pair hydrogen bond intensifies the intra GC base pair hydrogen bonding by approximately 2 kcal/mol for each GC pair in the tetrads.