Supercomputer simulation of the dynamics of oligomers of a number of amino acids (Gly, Ala, Trp, Val) in the infrared electromagnetic field

Supercomputer simulation of several amino acid oligomers using the molecular dynamics method has made it possible for the first time to identify a complex of characteristics of both intrinsic intramolecular local vibrations, or normal modes, and forced vibrations when specifying an alternating electric field in the IR frequency range. Amplitude-time dependences of energy and electric dipole moment were obtained for oligomers of Gly, Ala, Trp, Val amino acids, the Fourier transform of which revealed their frequency spectra. The type of solvent model was shown to significantly affect the position of spectral peaks because of variations in local interactions and system dynamics. The interpretation of the obtained patterns made it possible to propose a non-contradictory model that satisfied the fundamental physical concepts of the intramolecular and intermolecular dynamics of groups of biomolecules. The model allows for intramolecular interactions of normal local vibrations, including those of the Fermi resonance type.