The science gateway MoSGrid (Molecular Simulation Grid) is a valuable and user-friendly tool to submit and process molecular simulation studies on a large scale. With regard to the needs of the users, we focus on the comparability of simulations using two prominent quantum chemical codes, Gaussian09 and NWChem. At first sight, the definition of functionals and basis sets seems to be sufficient to evoke the same type of calculation in both codes using the quantum chemical workflows in MoSGrid. In the very detail, this is not true and more aspects such as integration grids, convergence criteria, basis set dimensions etc. Have to be defined in order to obtain a trustful comparability between quantum chemical codes. Up to now, these details have not been defined in the MSML (Molecular Simulation Mark up Language) implementation within MoSGrid. After the present investigation, all these details can be integrated to extend the quantum chemical workflows in MoSGrid.