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

Abstract

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 Ala_n (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.

Keywords::

• terahertz spectra
• molecular dynamics
• alanine polypeptides
• chain length
• conformation
• hydrogen bond

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was partially supported by National 973 Program of China [grant number 2015CB755401], National Natural Science Foundation of China [grant number 31400625] and [grant number 21407145], Fundamental & Advanced Research Project of Chongqing, China [cstc2013jcyjC00001] and Scientific Equipment Research Project of Chinese Academy of Sciences Development of THz imaging spectrometer for biomacromolecules.