Terebinska M. Quantum chemical simulation of adsorption of oxygen, water and pyridoxine on the surface of silicon

Quantum chemical calculations related to the equilibrium spatial structures of the complexes of O2 and H2O molecules adsorbed on the (111) and (100) faces of crystalline silicon were performed. Calculations were based on density functional theory and made use of the B3LYP method and the 6-31G** basis set. The energy of formation of the intermediate compounds and the values of the activation barriers for transitions between them were thus calculated. The heat released during the formation of all intermediate structures was calculated with the energy of activation barriers being taken into account. The exothermicity reflected the spontaneity of oxidation of the surface of crystalline silicon under the influence of molecular oxygen or water. The oxygen atoms that appear after dissociation of the adsorbed O2 molecule were found to form Si-O-Si bridges on the surface of crystalline silicon, that are adjacent to one silicon atom (the center of the subsequent attack of the oxygen molecule). This might confirm the insular nature of the oxidation process on the Si (111) and Si (100) faces. Frequencies and modes of normal vibration of the atoms in the adsorption complexes and surface compounds were calculated with the harmonic approximation. An essential difference was found between the vibrational frequencies of oxygen atoms in interstitial positions of the crystal lattice and the frequencies of adsorbed atomic and molecular oxygen. These results were confirmed by comparison with experimental available data. It was also found that the position of the bands in the calculated spectra is primarily dependent on the chemical surroundings of oxygen atoms, while the structure of the involved crystal faces plays only a secondary role. It was proved that the inclusion of the triplet ground state O2 molecule attacking the face of the Si (111) is essential for a correct description of its interaction, not only with the surface of crystalline silicon but also to any solid surface. The calculations revealed that the O2 molecules at distances greater than 0.35 nm from the Si (111) cluster are in the triplet state and perpendicularly oriented to the Si (111) plane. At 0.35 nm the surface influence would trigger the triplet-singlet transition. Thereafter the axis of the molecule would become parallel to the surface and the subsequent evolution of the (111)-O2 complex would follow a curve typical of a molecular adsorption complex. Calculations of the equilibrium spatial structure of the model of pyramidal formations on the surface of porous silicon were also performed. The distribution of the molecular electrostatic potential and the intensity module of the electrostatic field indicate that the electrostatic field near pyramidal formations has enough strength to enable the ionization of adsorbed organic molecules upon radiation with an external laser. The thus described approach was used to rationalize the mechanism of formation of protonated molecular ions of pyridoxine adsorbed on silica, during an experiment of laser ionization / desorption. The theoretical interpretation of the mass spectra of fragment ions was thus clarified.