Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interactio
n energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O and S are presented. The RMSD interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged specie, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than NDDO type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a requisite for
identifying intrinsic issues responsible for long range charge transfers. By merging density-functional-theory-based calculations and model-Hamiltonian approaches, we have studied DNA quantum transport during the stretching-twisting process of poly(GC) DNA oligomers. During the stretching process, local maxima in the charge transfer integral t between two nearest-neighbor GC pairs arise from the competition between stretching and twisting. This is reflected in local maxima for the conductance, which depend very sensitively on the coupling to the electrodes. In the case of DNA-electrode couplings smaller than t, the conductance versus stretching distance saturates to plateau in agreement with recent experimental observations.
