Molecular dynamics simulations were used to study relaxation of a vibrationally excited C6F6* molecule in a N2 bath. Ab initio calculations were performed to develop N2-N2 and N2-C6F6 intermolecular potentials for the simulations. Energy transfer from "hot" C6F6 is studied versus the bath density (pressure) and number of bath molecules. For the large bath limit, there is no heating of the bath. As C6F6* is relaxed, the average energy of C6F6* is determined versus time, i.e., ⟨E(t)⟩, and for each bath density ⟨E(t)⟩ is energy dependent and cannot be fit by a single exponential. In the long-time limit C6F6 is fully equilibrated with the bath. For a large bath and low pressures, the simulations are in the fixed temperature, independent collision regime and the simulation results may be compared with gas phase experiments of collisional energy transfer. The derivative d[⟨E(t)⟩]/dt divided by the collision frequency ω of the N2 bath gives the average energy transferred from C6F6* per collision ⟨ΔE(c)⟩, which is in excellent agreement with experiment. For the ~100-300 ps simulations reported here, energy transfer from C6F6* is to N2 rotation and translation in accord with the equipartition model, with no energy transfer to N2 vibration. The energy transfer dynamics from C6F6* is not statistically sensitive to fine details of the N2-C6F6 intermolecular potential. Tests, with simulation ensembles of different sizes, show that a relatively modest ensemble of only 24 trajectories gives statistically meaningful results.

In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and Hessian required from the simulation are obtained directly from the electronic structure theory. These simulations are extensively used to (1) interpret experimental results and understand the atomic-level dynamics of chemical reactions; (2) illustrate the ability of classical simulations to correctly interpret and predict chemical dynamics when quantum effects are expected to be unimportant; (3) obtain the correct classical dynamics predicted by an electronic structure theory; (4) determine a deeper understanding of when statistical theories are valid for predicting the mechanisms and rates of chemical reactions; and (5) discover new reaction pathways and chemical dynamics. Direct dynamics simulation studies are described for bimolecular S2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra. Also included are discussions of quantum effects, the accuracy of classical chemical dynamics simulation, and the methodology of direct dynamics.

Direct dynamics simulations, utilizing the RM1 semiempirical electronic structure theory, were performed to study the thermal dissociation of the doubly protonated tripeptide threonine-isoleucine-lysine ion, TIK(H), for temperatures of 1250-2500 K, corresponding to classical energies of 1778-3556 kJ/mol. The number of different fragmentation pathways increases with increase in temperature. At 1250 K there are only three fragmentation pathways, with one contributing 85% of the fragmentation. In contrast, at 2500 K, there are 61 pathways, and not one dominates. The same ion is often formed via different pathways, and at 2500 K there are only 14 m/z values for the product ions. The backbone and side-chain fragmentations occur by concerted reactions, with simultaneous proton transfer and bond rupture, and also by homolytic bond ruptures without proton transfer. For each temperature the TIK(H) fragmentation probability versus time is exponential, in accord with the Rice-Ramsperger-Kassel-Marcus and transition state theories. Rate constants versus temperature were determined for two proton transfer and two bond rupture pathways. From Arrhenius plots activation energies E and A-factors were determined for these pathways. They are 62-78 kJ/mol and (2-3) × 10 s for the proton transfer pathways and 153-168 kJ/mol and (2-4) × 10 s for the bond rupture pathways. For the bond rupture pathways, the product cation radicals undergo significant structural changes during the bond rupture as a result of hydrogen bonding, which lowers their entropies and also their E and A parameters relative to those for C-C bond rupture pathways in hydrocarbon molecules. The E values determined from the simulation Arrhenius plots are in very good agreement with the reaction barriers for the RM1 method used in the simulations. A preliminary simulation of TIK(H) collision-induced dissociation (CID), at a collision energy of 13 eV (1255 kJ/mol), was also performed to compare with the thermal dissociation simulations. Though the energy transferred to TIK(H) in the collisions is substantially less than the energy for the thermal excitations, there is substantial fragmentation as a result of the localized, nonrandom excitation by the collisions. CID results in different fragmentation pathways with a significant amount of short time nonstatistical fragmentation. Backbone fragmentation is less important, and side-chain fragmentation is more important for the CID simulations as compared to the thermal simulations. The thermal simulations provide information regarding the long-time statistical fragmentation.

Chemical dynamics simulations were performed to investigate collisional energy transfer from highly vibrationally excited azulene (Az*) in a N2 bath. The intermolecular potential between Az and N2, used for the simulations, was determined from MP2/6-31+G* ab initio calculations. Az* is prepared with an 87.5 kcal/mol excitation energy by using quantum microcanonical sampling, including its 95.7 kcal/mol zero-point energy. The average energy of Az* versus time, obtained from the simulations, shows different rates of Az* deactivation depending on the N2 bath density. Using the N2 bath density and Lennard-Jones collision number, the average energy transfer per collision ⟨ΔEc⟩ was obtained for Az* as it is collisionally relaxed. By comparing ⟨ΔEc⟩ versus the bath density, the single collision limiting density was found for energy transfer. The resulting ⟨ΔEc⟩, for an 87.5 kcal/mol excitation energy, is 0.30 ± 0.01 and 0.32 ± 0.01 kcal/mol for harmonic and anharmonic Az potentials, respectively. For comparison, the experimental value is 0.57 ± 0.11 kcal/mol. During Az* relaxation there is no appreciable energy transfer to Az translation and rotation, and the energy transfer is to the N2 bath.

A chemical dynamics simulation was performed to study low energy collisions between N 2 and a graphite surface. The simulations were performed as a function of collision energy (6.34 and 14.41 kcal/mol), incident polar angle (20−70°) and random azimuthal angle. The following properties were determined and analyzed for the N 2 + graphite collisions:(1) translational and rotational energy distributions of the scattered N 2 ; (2) distribution of the final polar angle for the scattered N 2 ; (3) number of bounces of N 2 on the surface before scattering. Direct scattering with only a single bounce is dominant for all incident angles. Scattering with multiple collisions with the surface becomes important for incident angles far from the surface normal. For trajectories that desorb, the parallel component of the N 2 incident energy is conserved due to the extremely short residence times of N 2 on the surface. For scattering with an incident energy of 6.34 kcal/mol, incident polar angle of 40°, and final polar angle of 50°the percentage incident energy loss is 29% from the simulations, while the value is 27% for a hard cube model used to interpret experiment (J. Phys.: Condes. Matter 2012, 24, 354001). The incident energy is primarily transferred to surface vibrational modes, with a very small fraction transferred to N 2 rotation. An angular dependence is observed for the energy transfer, with energy transfer more efficient for incident angles close to surface normal.