Silver nanoparticles are recognized for numerous physical, biological, and pharmaceutical applications. eir main uses in the medical field comprise diagnostic and therapeutic applications. In this project, the interaction between silver nanoparticles and the lipid layer of the skin was studied in order to know how nanoparticles behave when they are in contact with the skin. Energies of the silver nanoparticles were calculated through the optimization of silver clusters using density functional theory implemented in the Gaussian program 09W. Biological molecules such as glucose, stearic acid, palmitic acid, and quercetin present in coated nanoparticles and in the skin were also optimized. e silver clusters containing 6 atoms were proven to be the most stable complexes. Moreover, a study of molecular orbital describing HOMO interactions of the clusters was performed showing that the electronic density was around the silver cluster. Molecular dynamics simulation was performed using Abalone program. Silver nanoparticles seemed to have very good clearance properties in our molecular dynamics simulation because over a certain period of time, the silver cluster got far away from the biological molecules.