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Structural Origin of Copper Ion Containing Artificial DNA: A Density Functional Study

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posted on 25.12.2008, 00:00 by Toru Matsui, Hideaki Miyachi, Takeshi Sato, Yasuteru Shigeta, Kimihiko Hirao
In order to investigate an origin of structural stability of a copper ion containing artificial DNA, we evaluated the stacking energy between [H−Cu2+H] (H: hydroxypyridone) dimer by means of density functional theory (DFT) with an Anderson−Langreth−Lindqvist van der Waals (vdW) functional. The calculated distance between the copper ions is about 3.6 Å, which agrees well with the experimental data. Evaluated stacking energy is about 8−10 kcal/mol, which is slightly smaller than that of two base pairs in a natural B-DNA. This tendency does not change in [H−2H+H], which does not contain copper ions. These results indicate that the vdW interaction dominates the inter-base-pair interaction over spin−spin interaction, in contrast to a conjecture by an experimental group. According to the results by the open-shell DFT, antiferromagnetic (singlet) and ferromagnetic (triplet) states are almost degenerated when the two bases are vertically located and both bases have a planar structure as found in the B-DNA.