N1s and C1s Near-Edge X-ray Absorption Fine Structure Spectra of Model Systems for Pyridine on Si(100): A DFT Simulation

This work presents a density functional theory (DFT)-based computational investigation of the near-edge X-ray absorption fine structure (NEXAFS) spectra of pyridine on the Si(100) surface. The accurate modeling of the adsorbate system is tackled by a preliminary optimization of the surface and of the molecules adsorbed on it performed by a periodic slab methodology. From the optimized periodic structures, suitable finite clusters are then cut out and used for the calculation of core excitation energies and oscillator strengths of the adsorbed pyridine. Various adsorption modes are considered, and for each of them, the polarized spectra at the N K edge and the C K edge of the pyridine have been simulated with the transition potential scheme to include the core hole relaxation effect. Careful analysis of the calculated polarized features and the intensity trend with the change of polarization reveals important information on specific details of the adsorption geometries and supports the comparison with experiment. The XII, VII, IV on-dimer and cross-trench adsorption modes appear suitable to explain the experimental N1s features observed at low temperature, but they cannot account for all the experimental features emerging at room temperature in both the N1s and C1s spectra. To deal with this issue, the mode IX geometry is also considered for the presence of a -C=N- (imine) chemical group that appears to play an important role for the interpretation of N1s and C1s spectra at 300 K. The long-range effects of an extended surface model on the NEXAFS features is also analyzed and shows the importance of an accurate modeling of the Si(100) reconstructed surface for a confident simulation of the NEXAFS spectra of the adsorbed pyridine.