Dynamics of flexible peptides under the action of an electrostatic field in the gas phase

The Ion Mobility Spectrometry data of flexible peptides have been found to depend on the temperature of the buffer gas. It has been observed that the number of the peaks of the arrival time distribution may vary, while the position of the peaks may shift with temperature. Such changes depend on the emerging conformers at the experimental conditions. The motion and the dynamics of the peptide are reproduced here through a Nonequilibrium Molecular Dynamics Simulation procedure that depends on the structure of the bending macromolecule. A specific molecular model of one bending mode is considered that depends on an angular interaction potential. The observed conformations are introduced through the consideration of local minima in the model potential. As the molecular dynamics simulation proceeds, the population of the metastable structures is changing in time due to energy exchange during the ion-atom interactions. The corresponding angle distributions depend on the temperature and the field strength. We find that the observed motion of the peptide conformers can be reproduced accurately with the use of empirical model potentials and further predict the behavior of the ions at strong electric fields. The procedure can produce mean properties, such as the ion velocity and energy, as well as molecular distributions and dynamic properties, such as velocity correlation functions. We expect the method to apply to similar flexible macromolecules that acquire one bending mode.