Abstract
We report on our calculations of the inner-sphere reorganization energy and the interaction of the pi orbitals within DNA oligomers. The exponential decrease of the electronic coupling between the highest and second highest occupied base orbitals of the intrastrand nucleobases in the (A-T)n and (G-C)n oligomers have been found with an increase of the sequence number n in the DNA structure. We conclude that for realistic estimation of the electronic coupling values between the nucleobases within the DNA molecule, a DNA chain containing at least four base pairs is required. We estimate the geometry relaxation of the base pairs within the (A-T)n and (G-C)n oligomers (n=1-6) due to their oxidation. The decrease of the inner-sphere reorganization energy with elongation of the oligomer structure participating in the oxidation process have been observed. The maximum degree of geometry relaxation of the nucleobase structures and correspondingly the higher charge density in the oxidized state are found to be located close to the oligomer center.
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