Electronic Couplings Between Neighboring Pairs

In this section we will consider some examples of the electronic coupling between neighboring Wats on-Crick pairs, calculated in the two-state model. 

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This limitation has been overcome with a special NDDO-HT parameterization for calculating hole coupling matrix elements in DNA-related systems [72]. As reference data, coupling matrix elements were calculated for a set of 130 structures of WCP dimers with different step parameters at the HF/6-31G level. As discussed below in more detail, electronic couplings between neighboring pairs are extremely sensitive to conformational fluctuations of the DNA structure. For instance, the matrix element between base pairs in... 

If one attempts an accurate description of the coupling between neighboring pairs, one needs to answer several general questions. How accurate is the one-electron approximation How essential are the effects of electron corre-... 

Consider next the process, atom A -I- atom B —> atom A+4- atom B . The change in energy is U, the ionization potential minus the electron affinity (the energy to make the ion pair when the atoms are far apart), minus the Coulomb attraction between the two atoms a distance Rab apart, U = I.P. A) - E.A. B) - c IRab- Here, t is the strength of coupling of neighboring atoms when they are close. That s it there are no other parameters. 

These equations must be solved numerically. In our first calculations [46] the value of to was taken as 0.3 eV, the value obtained from an ab initio calculation of the energy of a pair of Gs as a function of the distance between them [47] for a separation of 3.4 A. The electron-phonon coupling constant a, the derivative of t with respect to displacement, was obtained as 0.6 eV/A from the results of [47]. Subsequently, when a value of to other than 0.3 eV was used a was scaled accordingly. Although to and a values depend on the particular pair of neighboring bases, the calculations were simplified by using the same value for all pairs of bases. The value of the elastic constant K was taken as 0.85 eVIA, derived [46] from the measured value of the sound velocity in DNA. 

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