I came across a publication by Senthilkumar et al.  in order to compute charge transfer through the DNA. Table 3, for instance, gives the coupling between bases along the leading (or retarded) strand of DNA:
Table 3. Charge-Transfer Integrals, $J$ (in eV), Overlap Matrix Elements, S, and Generalized Charge-Transfer Integrals, $J′$ (in eV), for Nucleobases Stacked at a Distance of 3.38 Å with a Twist Angle of 36°
For concreteness I will talk about only on columns 3 and 6 of the aforementioned table. I have two questions:
For instance, is it 5'-A-C-3' physically different from 5'-C-A-3'? If I 'erase' the direction 5' to 3', then A-C or C-A should be coupled by the same number (for instance, 0.042). However, I think that 5'-A-C-3' is different from 5'-C-A-3', because in the first example, a phosphate is "attached" to A from the left and a sugar is attached to C to the right; in the second case, C is attached to the phosphate to the left and A is attached to the sugar to the right. Is this interpretation correct?
5'-A-C-3' the coupling says it is 0.042, for 5'-C-A-3' it is −0.002. If I regard the previous argument as true, then both DNA systems are different, but not too different since they contain the same basis A and C. Does it make sense that by just changing the position of phosphates and sugars, one is approx. 40 times bigger than the other?
- Senthilkumar, K.; Grozema, F. C.; Guerra, C. F.; Bickelhaupt, F. M.; Lewis, F. D.; Berlin, Y. A.; Ratner, M. A.; Siebbeles, L. D. A. Absolute Rates of Hole Transfer in DNA. J. Am. Chem. Soc. 2005, 127 (42), 14894–14903. DOI: 10.1021/ja054257e.