In the first part of this thesis, the adsorption of cysteine (CYS) in the form of zwitterion (ZWCYS), cationic (CATCYS), uncharge (UNCYS), and anionic (ANCYS) on the metal nanoclusters including Au@Au12 , Ag@Au12 , Pd@Au12 , and Pt@Au12 was studied using density functional theory (DFT). Based on the obtained results, the type of the core metal atom has a considerable effect on the adsorption energy (Ead), interaction energy (Eint), adsorption configuration of the molecule, the strength of Au-S bond formed between the molecule and metal nanocluster, and charge transfer between molecule and metal nanocluster. The quantum theory of atoms in molecules (QTAIM) was used for the determination of the formed interaction paths between the different forms of CYS and the nanoclusters and the change of the strength of Au-S bond with the type of core metal atom. The effect of core metal atom on the IR spectrum of each form of CYS was studied and the vibrational bands which are sensitive to the type of metal cluster were determined. Also, the effect of water as a solvent on the adsorption and interaction of ZWCYS in three different conditions was investigated. These conditions are (a) considering the electrostatic field of solvent using the polarized continuum model (PCM) (b) microhydration of ZWCYS in the gas phase interacting with the metal nanoclusters to see the explicit effect of water molecules on the interaction and adsorption of ZWCYS in the absence of electrostatic field of water (c) considering both (a) and (b) conditions simultaneously. In the second part of the thesis, the absorption spectra of isolated metal nanoclusters ( Au@Au12 , Ag@Au12 , Pd@Au12 , and Pt@Au12 ) and their complexes with ZWCYS were calculated in the gas phase. The effect of the type of core atom and the interaction of ZWCYS with nanocluster on the intensity and the position of the maximum of absorption spectra of nanoclusters was investigated. The absorption lines responsible for the excitation charge transfer from the ZWCYS to metal nanoclusters were determined and their changes with the type of core atom were determined. The normal Raman and the Frequency-Dependent Near Resonance Raman (FDNRR) spectra of ZWCYS interacting with the nanoclusters were calculated. Vibrational bands of ZWCYS which show the increase of intensity in the FDNRR spectra due to the charge transfer were determined.
