Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections

Abstract

The extent of electronic wave function delocalization for the charge carrier (electron or hole) in double helical DNA plays an important role in determining the DNA charge transfer mechanism and kinetics. The size of the charge carrier’s wave function delocalization is regulated by the solvation induced localization and the quantum delocalization among the π stacked base pairs at any instant of time. Using a newly developed localized orbital scaling correction (LOSC) density functional theory method, we accurately characterized the quantum delocalization of the hole wave function in double helical B-DNA. This approach can be used to diagnose the extent of delocalization in fluctuating DNA structures. Our studies indicate that the hole state tends to delocalize among 4 guanine–cytosine (GC) base pairs and among 3 adenine–thymine (AT) base pairs when these adjacent bases fluctuate into degeneracy. The relatively small delocalization in AT base pairs is caused by the weaker π–π interaction. This extent of delocalization has significant implications for assessing the role of coherent, incoherent, or flickering coherent carrier transport in DNA.

Exact analytical ground state solution of 1D H$$_2^+$$ with soft Coulomb potential

“…This might shed light on the qualitative breakdown of many density functional approximations when the bond is stretched-they capture the essential physics of a compact molecule but has difficulty capturing the qualitatively different solution of a dissociated molecule. Interestingly, the exact solution appears to support the strategy of the recently developed localized orbital scaling correction (LOSC) functional [23][24][25][26][27][28][29] that treats the two situations differently. Furthermore, the form of the exact wave function could also inspire of better localization scheme in the LOSC framework.…”

Mapping of Charge Delocalization Domain in Fluctuating DNA

“…94 Voityuk et al used the correlations of onsite energies as well as the correlations of electronic couplings between neighboring base pairs to characterize hole size. 60,61,81,82,[95][96][97][98] The rationality of these work is supported by the analysis of the delocalized domain. Finally, the localized domains (πDI=0 in Figure 4) with large couplings and small σ ǫ values correspond the model of incoherent hopping.…”

“…41,44,58 And there are other debates on it. 43,78,81,95,97,98,108 In our model the hole size is fluctuated and the fluctuating range varies with the lengths of the delocalized domains ( Figure 6). It is the switch between delocalization/localization of a domain delivers a hole to the distant place.…”

“…From this point of view, a hole should be easier to be delocalized on A-sequence than on G-sequence, what is in line with current consensus. 50,104 Recently, Jin et al adopted the method of localized orbital scaling correction (LOSC) DFT to give a contrary result, 95 making it somewhat controversial in theory. But the electron spin resonance (ESR) experiments showed that the signal of hole delocalization on A-stack is more obvious than on G-stack.…”

Theoretical Modeling of Redox Potentials of Biomolecules

“…In fact, on the one hand, the structural–dynamical fluctuations of the systems might affect the redox properties, and, thus, they should be taken into account. On the other hand, it is not completely clear the nature of the electronic hole, which can be localized on a single nucleobase [ 147 , 148 ] or, alternatively, delocalized along the strand [ 149 , 150 ].…”