Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides

Terahertz absorption spectra of alanine polypeptides in water were simulated with classical molecular dynamics at 310 K. Vibrational modes and oscillator strengths were calculated based on a quasi-harmonic approximation. Absorption spectra of Alan (n = 5, 15, 30) with different chain lengths and Ala15 in coiled and helical conformations were studied in 10–40 cm− 1 bandwidth. Simulation results indicated both the chain length and the conformation have significant influences on THz spectra of alanine polypeptides. With the increase of chain length, the average THz absorption intensity increases. Compared with the helical Ala15 polypeptide, the THz spectra of coiled one shows stronger absorption peaks. These results were explained from different numbers of hydrogen bonds formed between polypeptides and the surrounding water molecules.

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