The structures and vibrational spectra of neutral and protonated adenine molecules were calculated at the B3LYP/aug-cc-pVTZ level. For neutral adenine, the N9H adenine configuration is more stable in energy of about 32.76 kJ . mol(-1) (6.28 kJ . mol(-1) by using the polarization continuous model (PCM)) than N7H adenine. Based on the potential energy distribution (PED) calculated using the scaled quantum mechanical field (SQMF) procedure, we corrected the assignments of some N9H adenine fundamental vibrations. There are five stable configurations for protonated adenine and the isomer of adenine that is protonated at the NI position is the most stable. Based on vibration analysis, we assigned the fundamental vibrations of this configuration and analyzed the Raman spectra of adenine in the HClO4 (pH=1) solution. ; National Natural Science Foundation of China [20573087]; National Key Basic Research Program of China [2007CB815303, 2009CB930703]; Program for New Century Excellent Talent (NCET) in Universities of Fujian Province, China