Instantaneous dipole moments of polyalanine peptides in vacuum and in the aqueous medium have been calculated on the picosecond time scale in order to evaluate the external influence of temperature, of the electrostatic field’s amplitude and direction. Computer simulation was performed using the molecular dynamics method. The dynamic scenarios induced by the external electrostatic field above 100 MV/m were obtained for polyalanine molecules of different lengths (from 2 to 24 groups) placed in vacuum and in aqueous medium, the time step of 1 fs and the simulation time up to 100 ns being taken. The simulated scenarios can be used for a further analysis and a generalized description of structural properties and conformational dynamics of molecules. The mastered software packages are appropriate for computing the representational scenarios of biomolecular behavior under various conditions.
Citation: T.I. Zezina, O.Yu. Tsybin, Subpicosecond dynamics of the molecular polyalanine dipole moment, St. Petersburg Polytechnical State University Journal. Physics and Mathematics. 10 (3) (2017) 100–110. DOI: 10.18721/JPM.10408