Potential energy function development and dynamics of energy transfer and fragmentation for collisions of protonated peptide ions with organic surfaces

The study of ion-surface collisions has been a subject of interest for the past few years. There are a number of processes observed for these type of collision depending on the translational energy. Projectile ions, with translational energies in the range of 1- 100 eV, adhere when they collide with organic surfaces. This is called soft-landing and by colliding biological molecules with surfaces, this property has been used to prepare microarrays. Chemical dynamics simulations give near quantitative energy transfer probabilities for projectile ion collisions with surfaces as compared to experimental results, and there is substantial interest to extend this work to soft-landing. However, to model these experiments it is necessary to have accurate short-range and long-range potentials for the projectile-surface interaction. The former controls the collisional energy transfer and the latter forms the gas-surface attraction. Developing the combined short-range and long-range potentials is one focus of this work. Potentials for the CH4-CH3NH3+ interaction were calculated at the MP2/aug-ccpVTZ level of theory, with a basis set superposition error (BSSE) correction included, and fit with novel models for atom-atom two-body interactions. Another process observed during ion-surface collisions is surface-induced dissociation (SID). The study of the SID of singly protonated octaglycine was done by perfoming direct dynamics trajectory simulations. The protonated octapeptide was allowed to collide with a diamond{111} surface and the trajectory simulations were performed using the VENUS/GAUSSIAN chemical dynamics package. These QM+MM direct dynamics simulations were carried out using the AM1 semi-empirical QM model for the intramolecular potential of the peptide ion. The simulations were performed for a collision energy of 100 eV and a collision angle of both 00 (normal to the surface) and 450. The energy transfer efficiencies were determined and compared with the experimental results of protonated des-arg-bradykinin which is also an octapeptide. The mechanism of fragmentation of the peptide ion was also studied and it was observed that a significant fraction occur via shattering as expected from experiments. The results are also compared with previous direct dynamics simulations of peptide-H+ SID.

Author dc:creator

• Deb, Bipasha

Contributors dc:contributor

• Gellene, Greg
• Hase, William L.

• Trajectory simulation
• Surface-induced dissociation (SID)
• Analytic

Statement dc:rights

• Unrestricted.

Language dc:language

eng

Identifier

http://hdl.handle.net/2346/11530

OAI identifier oai:identifier

oai:tdl-ir.tdl.org:2346/11530