Effect of guanine-cytosine base pair orientation and cluster size on ionization energy and charge distribution: A theoretical study

•Calculation of vertical ionization energies at different guanine-cytosine base pair orientation angles.•Density functional calculations of positive charge distribution in cationic guanine-cytosine clusters.•Guanine-cytosine cluster size and vertical ionization energies.•Prediction of product concentration in guanine sites in a hole transfer reaction.

Density functional calculations with B3LYP/aug-cc-pVDZ level of theory suggest that the vertical ionization energy (VIE) is minimum for 0° orientation angle of guanine-cytosine (GC)n (n = 2-6) base pairs, and maximum at around 30°, which is close to the natural base orientation angle (36°) in DNA. As the (GC)n cluster size is increased, the VIE value is decreased substantially from n = 1 to n = 3 (7.23-5.76 eV) followed by a less dramatic decrease for larger n values. In each cationic (GC)n cluster, the charge distribution among the G bases shows a pattern that depends upon odd or even number of base pairs in the cluster. At a very low temperature, when the orientation angle is frozen to its equilibrium value (around 36°), the CT rate is expected to drop significantly (large VIE value) in comparison with the rates at higher temperatures when small orientation angles are accessible with lower VIE values.

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