Short-Range Charge Transfer in DNA Base Triplets: Real-Time Tracking of Coherent Fluctuation Electron Transfer

Abstract

The short-range charge transfer of DNA base triplets has wide application prospects in bioelectronic devices for identifying DNA bases and clinical diagnostics, and the key to its development is to understand the mechanisms of short-range electron dynamics. However, tracing how electrons are transferred during the short-range charge transfer of DNA base triplets remains a great challenge. Here, by means of ab initio molecular dynamics and Ehrenfest dynamics, the nuclear-electron interaction in the thymine-adenine-thymine (TAT) charge transfer process is successfully simulated. The results show that the electron transfer of TAT has an oscillating phenomenon with a period of 10 fs. The charge density difference proves that the charge transfer proportion is as high as 59.817% at 50 fs. The peak position of the hydrogen bond fluctuates regularly between -0.040 and -0.056. The time-dependent Marcus-Levich-Jortner theory proves that the vibrational coupling between nucleus and electron induces coherent electron transfer in TAT. This work provides a real-time demonstration of the short-range coherent electron transfer of DNA base triplets and establishes a theoretical basis for the design and development of novel biological probe molecules.

Keywords: DNA base triplet; Ehrenfest dynamics; coherent electron transfer; nuclear-electron vibronic coupling; periodic oscillation.

Figure 1

(a) Structure of TAT base triplet. Blue: C; Orange: H; Pink: O; Purple: N. (b) Absorption spectrum of TAT base triplet. (c) The molecular orbitals involved in charge transfer. Blue for holes, and green for electrons. (d) Time evolution of molecular orbitals LUMO, LUMO + 1, and LUMO + 2 involved in coherent charge transfer process. (e) The distance between the donor and acceptor varies with time. (f) The electronegativity of N₁₀, N₁₅, and N₂₁ over time.

Figure 2

Graph of the function values of the TAT base triplet. The assignment of each peak on the gradient isosurface. The red circle marks the peak of the hydrogen bond.

Figure 3

Visualizing the time-dependent evolution of coherent charge transfer in TAT base triplets. Simulation of CDD evolution over time. The pink represents electrons, and the green represents holes.

Figure 4

The distribution of holes and electrons with time is observed by using the two-dimensional real space method. The TDM heat maps of the electron’s movement with time.

Figure 5

Dynamic evolution of hole–electron interaction analysis and Marcus theory of TAT base triplet with time. (a) The distribution of electrons (green) and holes (blue) over time. (b) The numerical variation of the electron–hole distance D and the corresponding Sr. (c) Dynamic evolution of numerical t of electron–hole separation degree. (d) The corresponding evolution of HDI and EDI. (e) Change in reorganization energy over time. (f) Evolution of free energy $\Delta G_{CT}$ and $\Delta G_{CR}$ over time.