Abstract: We present the fully optimized structures of 4-residue and 5-residue α-helices at the B3LYP/6-31+G** level in solvent. The calculated backbone conformations are in good agreement with the statistical results from protein crystal structures. Similar to long regular α-helices, the fraying of the C-teriminal is observed. For short polyalanine peptide, 310-helix is significantly more stable than α-helix in enthalpy. However, the 310-helix is destabilized by entropy effect. In addition, it has been found that the capping effect by an aspartic acid at N2(second residue from the N-terminal) significantly stabilizes the α-helix over the 310-helix. Thus, the statistics that there are more shortest α-helices than 310-helices of the same length can be understood. It has been also found that the C-terminal of the shortest α-helix tends to end with a β-turn structure.

Key words: α-Helix, 310-Helix, Density functional theory(DFT) calculation, H-bond capping