  In the past two decades, many research groups worldwide have tried to
understand and categorize simple regimes in the charge transfer of such
biological systems as DNA. Theoretically speaking, the lack of exact theories
for electron-nuclear dynamics on one side, and poor quality of the parameters
needed by model Hamiltonians and nonadiabatic dynamics alike (such as couplings
and site energies) on the other, are the two main difficulties for an
appropriate description of the charge transfer phenomena. In this work, we
present an application of a previously benchmarked and linear-scaling subsystem
DFT method for the calculation of couplings, site energies and superexchange
decay factors ($\beta$) of several biological donor-acceptor dyads, as well as
double stranded DNA oligomers comprised of up to 5 base pairs. The calculations
are all-electron, and provide a clear view of the role of the environment on
superexchange couplings in DNA - they follow experimental trends and confirm
previous semiempirical calculations. The subsystem DFT method is proven to be
an excellent tool for long-range, bridge-mediated coupling and site energy
calculations of embedded molecular systems.
