The adsorption on the TiO2 surface of two dipeptides AE (L-alanine-L-glutamic acid) and AK (L-alanine-L-lysine), that are "building blocks" of the more complex oligopeptide EAK16, has been investigated both theoretically and experimentally. Classical molecular dynamics simulations have been used to study the adsorption of H-Ala-Glu-NH2 and H-Ala-Lys-NH2 dipeptides onto a rutile TiO2 (110) surface in water solution. Several peptide conformers have been considered simultaneously upon the surface. The most probable contact points between the molecules and the surface have been identified. Carbonyl oxygens as well as nitrogen atoms are possible Ti coordination points. Local effects are responsible for adsorption and desorption events. Self-interaction effects can induce molecular reorientations giving less strongly adsorbed species. The chemical structure and composition of thin films of the two dipeptides AE and AK on TiO2 were investigated by XPS (X-ray photoelectron spectroscopy) measurements at both O and N K-edges. Theoretical ab initio calculations (Delta SCF) were also performed to simulate the spectra, allowing for a direct comparison between experiment and theory.