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Ab initio calculation was performed on the model peptide compound alanine dipeptide. The population of the secondary structures and the corresponding potential energies of alanine dipeptide were investigated. Normal mode analysis was performed on the amide vibrational modes, which are known to be quite sensitive to the molecular structure, and the correlation between the vibrational feature and the molecular structure was then revealed. The results show that alanine dipeptide has a minimum potential energy when the backbone dihedral is positioned at Φ/Ψ =-80°/80° , which can be denoted as a C7eq conformation. It is also possible to form the secondary structures with β sheet, PPII, C5, and C7 conformations for their low potential energies. The vibrational parameters of the 3N-6 vibrational motions were obtained through normal mode analysis. The amide vibrational modes were then assigned by the potential energy distribution analysis. The amide-I mode, mostly consisting of backbone C=O stretching, was introduced for the prediction of the secondary structure of alanine dipeptide. The correlation between the amide-I vibrational parameters and the molecular structures is then demonstrated. Thus is a new way for the prediction of structural features of peptide and protein systems at the chemical bond level.