Application of computational models to the study of molecular sensors

In the present work we have considered various topics concerning spectroscopic properties simulation (Part I) and basic aspects involved in nanoscience (Part II). In the first part the IR spectra of uracil in vacuo was simulated by the Fourier Transform of the dipole autocorrelation function. This function has been generated by the sampling of the 10 ps ADMP (ab initio Density Matrix Propagation) trajectory. The results were compared with the experimental spectra of uracil in argon matrix so as to reproduce as much as possible the neglect of intermolecular interaction characteristic of the current simulation conditions. Moreover, the results were also compared with frequencies calculations within harmonic and anharmonic approximations. In the second part we studied basic aspects related to the synthesis of DNA/RNA biosensors. Full characterization of 1-amino-3cyclopentene (ACP) reaction path along both chemical functionalities was reported outlying the effective competitiveness of both reactions on silicon surface reaction sites. Differently from others works mainly focused on a radicalic mechanism, here we found another mechanism of reaction based on the separation of charges in silicon surface dimer with no radicals formation. The reaction path through ACP double bond has been studied in collaboration with the Departement of Physics of the University of Naples "Federico II" in order to compare computational results obtained within density functional theory (DFT) with both Gaussian Type Orbitals and Plane Waves basis set functions. To simulate the Si(100)-2x1 surface we used both cluster and slab models. Furthermore, it has been considered a further step in the surface functionalization considering the product of reactions of sulfo-succinimidyl-4-(N-maleimidomethyl)-cyclohexane-1-carboxilate (SSMCC) and thio-oligonucleotide on the ACP hybrid surface.