A cartoon representation of the RM1 four-centered TS structure. models the N terminal of the peptide, while HCOCl models the –COCl head group of the SAM. Critical bond distances are given for RM1, (B3LYP), and [MP2], respectively. The blue, white, black, red, and purple colors identify nitrogen, hydrogen, carbon, oxygen, and chlorine, respectively.
A cartoon representation of the RM1 equilibrium geometry of gly2-H+ (+NH3–CH2–CO–NH–CH2–CO2H) obtained through optimization of the structure obtained from TINKER (Ref. 43). The blue, white, black, and red colors identify nitrogen, hydrogen, carbon, and oxygen atoms, respectively.
Frozen potential scans and the simultaneous fits to these limiting configurations. The ab initio data clearly shows that repulsive interactions dominate. The fits to two body Buckingham potential terms faithfully reproduce that behavior. The four orientations are labeled according to the interaction for which they emphasize.
Schematic diagram of the chemically modified F-SAM surface. The two embedded QM regions in the surface, a single chain (red box) and the single chain with a QM buffer region (blue box), are also depicted. Only the propyl tip of a chain is present in the QM region with the last CF2 group acting as a linking atom shown in green above. The chemically modified chain consists of the propyl tip substituted with either the –COCl or –CHO head group.
The fraction of peptide fragmentation, without peptide-surface reactivity, which occurs by shattering. Results are given for gly2-H+ colliding with both COCl-SAM and CHO-SAM.
The collision energy dependence of different peptide and surface fragmentation and reaction events. Surface fragmentation includes any trajectory for which a bond (or bonds) between C, F, and O atoms of the surface rupture. Peptide fragmentation includes trajectories for which a bond (or bonds) of the peptide backbone ruptures. Reactivity is defined to be the formation of a bond between a QM atom of the surface and a QM atom of the peptide. These are nonexclusive events and it is possible for all three to occur in the same trajectory. The COCl-SAM and the CHO-SAM display similar results for all but surface fragmentation which is much more likely for the CHO-SAM.
The collision energy dependence of specific reaction classes of gly2-H+ reaction with the SAM surfaces. See Sec. ??? for a detailed description of each class. Dramatic differences are seen due to the chemical identity of the head group.
Enthalpy barriers for gly-H+ and gly2-H dissociation.a
Parameters for two-body potential energy function between head groups and surface.
Dominant peptide fragmentation pattern percentages vs collision energy for trajectories without reaction with the surface.a
Most probable peptide-surface reactions and their heats of reaction for gly2-H+ + COCl-SAM.
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