• Energy Research

Different simulation approaches like MM, QM + MM, and QM/MM, were used to study surface-induced dissociation, soft-landing, and reactive-landing for the peptide-H++ surface collisions.

In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.

Results are reported for a direct dynamics simulation of NH(4)(+) + CH(4) gas phase collisions. We interpret the results with protonated peptide/hydrogenated alkanethiolate self-assembled monolayer (H-SAM) surface collisions in mind. Previous theoretical studies of such systems have made use of nonreactive surfaces, and therefore, our goal is to investigate the types and likelihood of peptide/H-SAM reactions. In that vein, the NH(4)(+) + CH(4) reaction represents a simple gas phase system which includes many of the important interactions present in protonated peptide/H-SAM surfaces. Thirty-seven open pathways are seen in the 5-35 eV collision energy range. An energy dependence on the likelihood of forming CN bonds is found. This type of bonding could deposit both the peptide and its molecular fragments on the H-SAM surface. For our gas phase collision system, around 50% of the trajectories result in the formation of CN bonds. For all collision energies in which reactive scattering occurs, CN bond formation is an important reaction pathway.

Results are reported for PM3 and RM1 QM+MM direct dynamics simulations of collisions of N-protonated octaglycine (gly(8)-H(+)) with an octanethiol self-assembled monolayer (H-SAM) surface. Detailed analyses of the energy transfer, fragmentation, and conformational changes induced by the collisions are described. Extensive comparisons are made between the simulations and previously reported experimental studies. Good agreement between the two semiempirical methods is found regarding energy transfer, while differences are seen for their fragmentation time scales. Trajectories were calculated for 8 ps with collision energies from 5 to 110 eV and incident angles of 0 degrees and 45 degrees. A linear relationship is found between the collision energy and key parameters of the final internal energy distributions of both gly(8)-H(+) and the H-SAM. In general wider distributions are seen for the H-SAM than for the peptide ion. An incident angle of 45 degrees leads to more energy transfer to the peptide, with wider distributions. The average percentage energy transfer to gly(8)-H(+) is nearly independent of the collision energy, while the average percentage transfer to the surface increases with collision energy. For normal incidence, we find an average percentage energy transfer to gly(8)-H(+) which is in excellent agreement with the experimentally measured value 10.1 +/- 0.8% for the octapeptide des-Arg(1)-bradykinin [J. Chem. Phys. 2003, 119, 3414]. At each collision energy dramatic conformational changes of gly(8)-H(+) are seen. The initial folded structure rearranges to form a beta-sheet like structure showing that the collision induces peptide unfolding. This process is more pronounced at an incident angle of 45 degrees. Following the conformation change, nonshattering fragmentation, promoted by proton transfer, is observed at the highest collision energies. Substantially more fragmentation occurs for the RM1 simulations.