The collision between gly8-H+ and an octanethiol self-assembled monolayer(H-SAM) is shown above. During the collision, energy is transfered from translational motion and into internal degrees of freedom. This allows for conformational changes to take place. In the above collision this results in an "unfolding" of the peptide to form a straight-chain structure. Fragmentation eventually takes place if a large enough quantity of energy is transfered to the peptide. This is illustrated below for the gly2-H+ + F-SAM system.

The fragmentation takes place after a delay, however it is also possible for "shattering" fragmentation to take place.

This particular F-SAM system also includes the chemical modification of a COCl head-group placed on the center chain. This allows for the possibility of a chemical reaction to take place.

In this case, the Cl-atom functions as a leaving group and forms rotationally excited HCl. Concurrently a covalent bond forms between the SAM and the peptide resulting in a modified surface. More complex dynamics and reactivity is also possible.

Here peptide fragmentation and reactivity take place at the same time. Also, rather than the Cl-atom leaving with a H-atom, it leaves with a fragment of the peptide.