A density functional theory (DFT) approach was used to investigate the interaction of cystine with Cu9 cluster at B3LYP/LANL2DZ/6-311++G(d,p) level of theory. It was observed that cystine interacts with copper cluster majorly through its disulfide and –COOH groups. The simulated Raman spectrum confirmed the cleavage of disulfide linkage by the disappearance of the –S-S- stretching mode, in good agreement with the earlier reported experimental study. As noted by the peaks observed due to Cu-S and Cu-O stretching mode in the simulated Raman spectrum, cystine is inferred to have chemisorbed on Cu9. Using NBO analysis, it was revealed that oxygen and sulfur donate electron pairs to copper in the Cu9-cystine system. Additionally, the MK[ESP] charge and FMO analysis supported the above mentioned results significantly.