This thesis deals with the prediction of the spatial distribution and diffusive dynamics of perfluorinated alkane molecules within a phospholipid bilayer by means of molecular dynamics simulations. Perfluorinated molecules exhibit a special type of philicity (fluorophilicity). This special feature makes perfluorinated molecules an interesting agent for insertion into lipid bilayers. A particular spotlight is put on the effect of adding a further functionality (an acidic and an alcoholic end-group) on the properties of the alkanes within the dipalmitoylphosphatidylcholine (DPPC) membrane which is fully solvated in liquid water. The aim of this project is to elucidate the complex interplay of the lipophilic core and the hydrophilic polar head groups of the lipid bilayer with the functionalized fluorophilic alkane molecules. During their interactions, the longer chain molecules showed faster penetration with a reduction in their translational and rotational movement and also shows clustering phenomenon. Dynamical observations such as an increase of the order parameters and gauche-trans conformations, related to the alkyl chains of the lipid bilayer were also computed. On the basis of information obtained from the density profiles and significant reduction of Area/Lipid, one can observe, phase transition of the lipid.