The vibrational properties of cyclohexene-2-ethanamine molecule are studied by both theoretically and experimentally. The theoretical calculations are performed using density functional perturbation theory (DFPT) based on plane wave pseudopotential method while the experimental technique is infrared (IR) spectroscopy. We also present the results of theoretical calculation of STM images for electron density of the cyclohexene-2-ethanamine. Our results also show that DFPT can be applied to the molecular systems in GGA approximation by comparing experimental and other commercial theoretical methods. (C) 2007 Elsevier B.V. All rights reserved.