Protonated Glycine Surface-Induced Dissociation

Surface-induced dissociation (SID) ° is an important experimental tool for determining structural properties of ions and energetic and mechanistic information concerning their dissociation pathways. In SID the ion is energized by collision with a surface. If electronic excitation is unimportant, the collision translational energy E, is partitioned between the final translational energy Ef, and transfer to the internal vibrational/rotational modes of the ion AEint and the vibrations of the surface 

The potential energy function used for the (gly-H) /diamond 111 system is given by 

The classical trajectory simulations were carried out with VENUS interfaced with the semiempirical electronic structure theory computer program MOPAC. To simulate experimental conditions for (gly-H) -I-diamond collisions, the center of a beam of (gly-H)+ ion projectiles is aimed at the center of the surface, with fixed incident angle 0, and fixed initial translational energy, E,. The radius of the beam was chosen so that the beam overlapped a unit area on the surface. For each trajectory, the projectile was randomly placed in the cross section of this beam and then randomly rotated about its center of mass so that it had an initial random orientation with respect to the surface. The azimuthal angle, %, between the beam and a fixed plane perpendicular to the surface, was sampled randomly between 0 and 2n. Such a random sampling of X simulates collisions with different domains of growth on the diamond surface. 

The initial conditions for the vibrational modes of the (gly-FI)+ were chosen via the quasiclassical normal-mode method, with the energy for each normal mode of vibration selected from the mode s 300 K harmonic oscillator Boltzmann distribution. A 300 K rotational energy of RT/2 was added to each principal axis of rotation of the projectile. Initial conditions for the diamond surface were chosen by first equiHbrating the surface to a 300 K Boltzmann distribution with 2 ps of molecular dynamics and scaHng the atomic velocities. The structure and atomic velocities obtained from this equilibration process are then used as the initial conditions for an equilibration run at the beginning of each trajectory. 

One hundred trajectories were calculated to simulate the fragmentation dynamics of (gly-H)+ energized by collision with the diamond 111 surface at , = 70 eV and 0, = 45°. Each trajectory was integrated for 1.5 ps or imtil 

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Park K, Song K, Hase WL (2007) An ab initio direct dynamics simulation of protonated glycine surface-induced dissociation, hit J Mass Spectrom 265 326-336... 

Meroueh O, Wang Y, Hase WL (2002) Direct dynamics simulations of collision- and surface-induced dissociation of N-protonated glycine. Shattering fragmentation. J Phys Chem A 106 9983-9992... 

Simulations of Collision- and Surface-Induced Dissociation of N-Protonated Glycine. Shattering Fragmentation. 

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