We study Rabi oscillations in a two-level system within the semiclassical approximation as an archetype test field of the Averaging Method (AM). The population transfer between the two levels is approached within the first and the second order AM. We systematically compare AM predictions with the rotating wave approximation (RWA) and with the complete numerical solution utilizing standard algorithms (NRWA). We study both the resonance (Δ = 0) and out-of-resonance () cases, where Δ = ω − Ω, and ℏΩ = E 2 − E1 is the two-level energetic separation, while ω is the (cyclic) frequency of the electromagnetic field. We introduce three types of dimensionless factors ϵ, i.e., ΩR/Δ, ΩR/Σ, and ΩR/ω, where ΩR is the Rabi (cyclic) frequency and Σ = ω + Ω and explore the range of ϵ where the AM results are equivalent to NRWA. Finally, by allowing for a phase difference in the initial electron wave functions, we explore the prospects coherence can offer. We illustrate that even with equal initial probabilities at the two levels, but with phase difference, strong oscillations can be generated and manipulated.

To describe the molecular electronic structure of nucleic acid bases and other heterocycles, we employ the Linear Combination of Atomic Orbitals (LCAO) method, considering the molecular wave function as a linear combination of all valence orbitals, i.e., 2s, 2px, 2py, 2pz orbitals for C, N, and O atoms and 1s orbital for H atoms. Regarding the diagonal matrix elements (also known as on-site energies), we introduce a novel parameterization. For the non-diagonal matrix elements referring to neighboring atoms, we employ the Slater–Koster two-center interaction transfer integrals. We use Harrison-type expressions with factors slightly modified relative to the original. We compare our LCAO predictions for the ionization and excitation energies of heterocycles with those obtained from Ionization Potential Equation of Motion Coupled Cluster with Singles and Doubles (IP-EOMCCSD)/aug-cc-pVDZ level of theory and Completely Normalized Equation of Motion Coupled Cluster with Singles, Doubles, and non-iterative Triples (CR-EOMCCSD(T))/aug-cc-pVDZ level of theory, respectively, (vertical values), as well as with available experimental data. Similarly, we calculate the transfer integrals between subsequent base pairs, to be used for a Tight-Binding (TB) wire model description of charge transfer and transport along ideal or deformed B-DNA. Taking into account all valence orbitals, we are in the position to treat deflection from the planar geometry, e.g., DNA structural variability, a task impossible for the plane Hückel approach (i.e., using only 2pz orbitals). We show the effects of structural deformations utilizing a 20mer evolved by Molecular Dynamics.

Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diversefields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem,to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages.Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.