  We implement a bottom-up multiscale approach for the modeling of defect
localization in $C_{6n^2}H_{6n}$ islands, i.e. graphene quantum dots with a
hexagonal symmetry, by means of density functional and semiempirical
approaches. Using the \textit{ab initio} calculations as a reference, we
recognize the theoretical framework under which semiempirical methods describe
adequately the electronic structure of the studied systems and thereon proceed
to the calculation of quantum transport within the non-equilibrium Green's
function formalism. The computational data reveal an impurity-like behavior of
vacancies in these clusters and evidence the role of parameterization even
within the same semiempirical context. In terms of conduction, failure to
capture the proper chemical aspects in the presence of generic local
alterations of the ideal atomic structure results in an improper description of
the transport features. As an example, we show wavefunction localization
phenomena induced by the presence of vacancies and discuss the importance of
their modeling for the conduction characteristics of the studied structures.
