We implement a bottom-up multiscale approach for the modeling of defect localization in C 6n 2 H 6n islands, ie graphene quantum dots with a hexagonal symmetry, by means of density functional and semiempirical approaches. Using the ab initio calculations as a reference, we recognize the theoretical framework under which semiempirical methods adequately describe the electronic structure of the studied systems and thereon proceed to the calculation of quantum transport within the nonequilibrium Green 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 …