The DFT-MD simulations were performed using the CASTEP package and the GGA-PW91 approximation. The core electrons are represented by ultrosoft pseudopotentials, with plane wave cutoff energies of 300 eV. The simulation system contains three layers of hydrogen-terminated Si (111) covered by a 3T thin film that consists of four polythiophene oligomers. The distance between the oligomers in the film is about 3.2 Å. The dimensions of the entire Si-substrate and thiophene thin film are 13.3 Å × 15.4 Å × 25 Å and contain a total of 220 atoms. The system is allowed to equilibrate for 200 ps prior to thiophene deposition.
      Two sets of deposition simulations are considered. In the first set two thiophene molecules are deposited with incident energies of 25 eV/molecule. In the second set of simulations, one thiophene molecule is deposited with an incident energy of 50 eV/ion. The simulation timestep is 1 fs and the simulations are allowed to evolve for about 240 fs/collision event.

      When the incident molecules impact the thiophene thin film, they break apart and chemically modify the structure of the oligomers. During this process, their kinetic energy is transferred to the oligomer film, which produces many energetic fragments and a collision cascade. Most of the energetic fragments that are produced at incident energies of 25 eV/molecule remain trapped between the top and bottom oligomer layers, while most of the energetic fragments that are produced at incident energies of 50 eV/molecule are trapped between the Si surface and bottom layer of the oligomer thin film. This is a reflection of the fact that the higher energy deposition process produces more chemical products that bond to the Si substrate, while the lower energy deposition process produces more chemical products that bond to the polythiophene oligomers.

      Before deposition all the carbon atoms in the system are sp²-hybridized. Examination of the change in the number of sp²-hybridized carbon atoms is one way to characterize the extent of system chemical modification as a result of deposition. After one thiophene molecule is deposited at 25 eV/molecule, the vast majority (90%) of the system carbon atoms are sp²-hybridized, which indicates only minor chemical modification. However, after two thiophene molecules are deposited at 25 eV/molecule, only 70 % of the system carbon atoms are sp²-hybridized. The simulations thus show that as the deposition process progresses, the damage to the thiophene film increases.