Ab initio molecular dynamics (AIMD) with density functional theory was applied to explore conformational motions and collisional cross section of folded and extended conformers of double charged peptide ions. Even though we were able to show that AIMD trajectory calculations reveal fast stages of conformational unfolding and refolding in conformers occurring within ca. 4 ps, we also proved that their thermal breathing had very minor effects on their collision cross sections. This indicates that equilibrium structures obtained from electron structure calculations and referring to 0 K can provide theoretical collision cross sections that closely approximate those pertinent to ambient temperature. This paper is published in the Journal of Physical Chemistry Letters and can be found here.
