Classical trajectory simulations are performed to study the efficiency of energy transfer in the collisional activation of polyglycine and polyalanine peptide ions with β-sheet and α-helix structures. Energy-transfer efficiencies for collisions with Ar are determined versus impact parameter, peptide size and structure, mass of the collider, the collision energy, and the form of the intermolecular potential between the peptide and argon. High-level ab initio calculations, for Ar interacting with small molecules representing the peptides' functional groups, are performed to determine an accurate Ar + peptide intermolecular potential. Energy transfer may be efficient 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 increases. However, at higher energies, an apparent impulsive energy-transfer regime is reached where the peptide size has a negligible effect on the energy-transfer efficiency. For a certain peptide size, structure may have a significant effect on energy transfer; i.e., α-helix peptide structures tend to be activated more efficiently than are β-sheet structures. Heavy rare-gas atoms such as Kr and Xe are much more efficient collision activators than a light collider like He. The form of the collision's repulsive intermolecular potential has a strong influence on the energy-transfer efficiency. Collisional energy transfer to peptide rotational energy is not insignificant and at high collision impact parameters may surpass energy transfer to peptide vibration. For many of the trajectories there are multiple encounters between the collider and peptide during a collision.