Collisional activation of small peptides

Classical trajectory simulations are performed to study the efficiency of e nergy transfer in the collisional activation of polyglycine and polyalanine peptide ions with beta-sheet and ct-helix structures. Energy-transfer effi ciencies for collisions with Ar are determined versus impact parameter, pep tide size and structure, mass of the collider, the collision energy, and th e form of the intermolecular potential between the peptide and argon. High- level ab initio calculations, for Ar interacting with small molecules repre senting the peptides' functional groups, are performed to determine an accu rate Ar + peptide intermolecular potential. Energy transfer may be efficien t and in some cases as high as 80%. There is a low collision energy regime in which the percent energy transfer increases as the peptide size increase s. However, at higher energies, an apparent impulsive energy-transfer regim e is reached where the peptide size has a negligible effect on the energy-t ransfer efficiency. For a certain peptide size, structure may have a signif icant effect on energy transfer; i.e., alpha-helix peptide structures tend to be activated mon efficiently than are beta-sheet structures. Heavy rare- gas atoms such as Kr and Xe are much more efficient collision activators th an a light collider like He. The form of the collision's repulsive intermol ecular potential has a strong influence on the energy-transfer efficiency. Collisional energy transfer to peptide rotational energy is not insignifica nt and at high collision impact parameters may surpass energy transfer to p eptide vibration. For many of the trajectories there are multiple encounter s between the collider and peptide during a collision.