The Destination

It is sometimes difficult to realize that you are making progress, especially in medical school. You fight your way through the dark woods, getting scratched by loose branches, not quite sure if your feet are pointed in the right direction. Sometimes the journey feels like the mountain is collapsing, your feet are falling under you, your fingers throb from frost bite. Yet, there are the days where you stop and see the beauty of the journey in front of you. The winter is not always a cold, barren place, it holds so much beauty and it is worth the fight to continue

Understanding Energy Transfer in Gas–Surface Collisions from Gas-Phase Models

Large-scale trajectory simulations of different projectiles colliding with an organic surface, as well as a gas–surface model for energy transfer, are employed to investigate the effects of the mass, size, shape, and vibrational frequency­(ies) of the projectile and of the projectile–surface interaction potential on the energy-transfer dynamics. The gas–surface model employed in this work relies on simple gas-phase scattering models. When energy transfer is analyzed in the limit of high incident energies, the following results are found in this study. The percent of energy transfer to vibration (and rotation) of light diatomic projectiles decreases as the projectile’s mass increases, while this transfer is almost independent of the mass for heavier projectiles. Transfer to final translation of diatomic projectiles is a U-shaped function of the projectile’s mass, as predicted by the hard cube model. For larger projectiles, the partitioning of the energy transferred to the internal degrees of freedom (dof) between vibration and rotation depends on the projectile’s size. In other words, transfer to rotation is more important for the smaller projectiles, while transfer to vibration dominates for the bigger ones, which have more vibrational dof. For small projectiles (less than 10 atoms), transfer to vibration increases as a function of the projectile’s size. However, for larger projectiles, the percent transfer to vibration is nearly constant, a result that can be attributed to a mass effect and also to the fact that only a reduced subset of “effective” vibrational dof is being activated in the collisions. For linear hydrocarbons colliding with the perfluorinated self-assembled monolayer (F-SAM), the number of “effective” modes was estimated to be around 18, which corresponds to a percent energy transfer to vibration of 20–22%. The percent transfer to vibration of the more compact cyclic molecules is a bit higher than that for their linear counterparts

How a Solvent Molecule Affects Competing Elimination and Substitution Dynamics. Insight into Mechanism Evolution with Increased Solvation

Competiting S_N2 substitution and E2 elimination reactions are of central importance in preparative organic synthesis. Here, we unravel how individual solvent molecules may affect underlying S_N2/E2 atomistic dynamics, which remains largely unclear with respective to their effects on reactivity. Results are presented for a prototype microsolvated case of fluoride anion reacting with ethyl bromide. Reaction dynamics simulations reproduce experimental findings at near thermal energies and show that the E2 mechanism dominates over S_N2 for solvent-free reaction. This is energetically quite unexpected and results from dynamical effects. Adding one solvating methanol molecule introduces strikingly distinct dynamical behaviors that largely promote the S_N2 reaction, a feature which attributes to a differential solute–solvent interaction at the central barrier that more strongly stabilizes the transition state for substitution. Upon further solvation, this enhanced stabilization of the S_N2 mechanism becomes more pronounced, concomitant with drastic suppression of the E2 route. This work highlights the interplay between energetics and dynamics in determining mechanistic selectivity and provides insight into the impact of solvent molecules on a general transition from elimination to substitution for chemical reactions proceeding from gas- to solution-phase environments

How a Solvent Molecule Affects Competing Elimination and Substitution Dynamics. Insight into Mechanism Evolution with Increased Solvation

Competiting S_N2 substitution and E2 elimination reactions are of central importance in preparative organic synthesis. Here, we unravel how individual solvent molecules may affect underlying S_N2/E2 atomistic dynamics, which remains largely unclear with respective to their effects on reactivity. Results are presented for a prototype microsolvated case of fluoride anion reacting with ethyl bromide. Reaction dynamics simulations reproduce experimental findings at near thermal energies and show that the E2 mechanism dominates over S_N2 for solvent-free reaction. This is energetically quite unexpected and results from dynamical effects. Adding one solvating methanol molecule introduces strikingly distinct dynamical behaviors that largely promote the S_N2 reaction, a feature which attributes to a differential solute–solvent interaction at the central barrier that more strongly stabilizes the transition state for substitution. Upon further solvation, this enhanced stabilization of the S_N2 mechanism becomes more pronounced, concomitant with drastic suppression of the E2 route. This work highlights the interplay between energetics and dynamics in determining mechanistic selectivity and provides insight into the impact of solvent molecules on a general transition from elimination to substitution for chemical reactions proceeding from gas- to solution-phase environments

How a Solvent Molecule Affects Competing Elimination and Substitution Dynamics. Insight into Mechanism Evolution with Increased Solvation

Competiting S_N2 substitution and E2 elimination reactions are of central importance in preparative organic synthesis. Here, we unravel how individual solvent molecules may affect underlying S_N2/E2 atomistic dynamics, which remains largely unclear with respective to their effects on reactivity. Results are presented for a prototype microsolvated case of fluoride anion reacting with ethyl bromide. Reaction dynamics simulations reproduce experimental findings at near thermal energies and show that the E2 mechanism dominates over S_N2 for solvent-free reaction. This is energetically quite unexpected and results from dynamical effects. Adding one solvating methanol molecule introduces strikingly distinct dynamical behaviors that largely promote the S_N2 reaction, a feature which attributes to a differential solute–solvent interaction at the central barrier that more strongly stabilizes the transition state for substitution. Upon further solvation, this enhanced stabilization of the S_N2 mechanism becomes more pronounced, concomitant with drastic suppression of the E2 route. This work highlights the interplay between energetics and dynamics in determining mechanistic selectivity and provides insight into the impact of solvent molecules on a general transition from elimination to substitution for chemical reactions proceeding from gas- to solution-phase environments

How a Solvent Molecule Affects Competing Elimination and Substitution Dynamics. Insight into Mechanism Evolution with Increased Solvation

Competiting S_N2 substitution and E2 elimination reactions are of central importance in preparative organic synthesis. Here, we unravel how individual solvent molecules may affect underlying S_N2/E2 atomistic dynamics, which remains largely unclear with respective to their effects on reactivity. Results are presented for a prototype microsolvated case of fluoride anion reacting with ethyl bromide. Reaction dynamics simulations reproduce experimental findings at near thermal energies and show that the E2 mechanism dominates over S_N2 for solvent-free reaction. This is energetically quite unexpected and results from dynamical effects. Adding one solvating methanol molecule introduces strikingly distinct dynamical behaviors that largely promote the S_N2 reaction, a feature which attributes to a differential solute–solvent interaction at the central barrier that more strongly stabilizes the transition state for substitution. Upon further solvation, this enhanced stabilization of the S_N2 mechanism becomes more pronounced, concomitant with drastic suppression of the E2 route. This work highlights the interplay between energetics and dynamics in determining mechanistic selectivity and provides insight into the impact of solvent molecules on a general transition from elimination to substitution for chemical reactions proceeding from gas- to solution-phase environments

How a Solvent Molecule Affects Competing Elimination and Substitution Dynamics. Insight into Mechanism Evolution with Increased Solvation

Competiting S_N2 substitution and E2 elimination reactions are of central importance in preparative organic synthesis. Here, we unravel how individual solvent molecules may affect underlying S_N2/E2 atomistic dynamics, which remains largely unclear with respective to their effects on reactivity. Results are presented for a prototype microsolvated case of fluoride anion reacting with ethyl bromide. Reaction dynamics simulations reproduce experimental findings at near thermal energies and show that the E2 mechanism dominates over S_N2 for solvent-free reaction. This is energetically quite unexpected and results from dynamical effects. Adding one solvating methanol molecule introduces strikingly distinct dynamical behaviors that largely promote the S_N2 reaction, a feature which attributes to a differential solute–solvent interaction at the central barrier that more strongly stabilizes the transition state for substitution. Upon further solvation, this enhanced stabilization of the S_N2 mechanism becomes more pronounced, concomitant with drastic suppression of the E2 route. This work highlights the interplay between energetics and dynamics in determining mechanistic selectivity and provides insight into the impact of solvent molecules on a general transition from elimination to substitution for chemical reactions proceeding from gas- to solution-phase environments

How a Solvent Molecule Affects Competing Elimination and Substitution Dynamics. Insight into Mechanism Evolution with Increased Solvation

Competiting S_N2 substitution and E2 elimination reactions are of central importance in preparative organic synthesis. Here, we unravel how individual solvent molecules may affect underlying S_N2/E2 atomistic dynamics, which remains largely unclear with respective to their effects on reactivity. Results are presented for a prototype microsolvated case of fluoride anion reacting with ethyl bromide. Reaction dynamics simulations reproduce experimental findings at near thermal energies and show that the E2 mechanism dominates over S_N2 for solvent-free reaction. This is energetically quite unexpected and results from dynamical effects. Adding one solvating methanol molecule introduces strikingly distinct dynamical behaviors that largely promote the S_N2 reaction, a feature which attributes to a differential solute–solvent interaction at the central barrier that more strongly stabilizes the transition state for substitution. Upon further solvation, this enhanced stabilization of the S_N2 mechanism becomes more pronounced, concomitant with drastic suppression of the E2 route. This work highlights the interplay between energetics and dynamics in determining mechanistic selectivity and provides insight into the impact of solvent molecules on a general transition from elimination to substitution for chemical reactions proceeding from gas- to solution-phase environments

Anharmonic Densities of States for Vibrationally Excited I^–(H₂O), (H₂O)₂, and I^–(H₂O)₂

Monte Carlo sampling calculations were performed to determine the anharmonic sum of states, <i>N</i>_anh(<i>E</i>), for I^–(H₂O), (H₂O)₂, and I^–(H₂O)₂ versus internal energy up to their dissociation energies. The anharmonic density of states, ρ_anh(<i>E</i>), is found from the energy derivative of <i>N</i>_anh(<i>E</i>). Analytic potential energy functions are used for the calculations, consisting of TIP4P for H₂O···H₂O interactions and an accurate two-body potential for the I^–···H₂O fit to quantum chemical calculations. The extensive Monte Carlo samplings are computationally demanding, and the use of computationally efficient potentials was essential for the calculations. Particular emphasis is directed toward I^–(H₂O)₂, and distributions of its structures versus internal energy are consistent with experimental studies of the temperature-dependent vibrational spectra. At their dissociation thresholds, the anharmonic to harmonic density of states ratio, ρ_anh(<i>E</i>)/ρ_h(<i>E</i>), is ∼2, ∼ 3, and ∼260 for I^–(H₂O), (H₂O)₂, and I^–(H₂O)₂, respectively. The large ratio for I^–(H₂O)₂ results from the I^–(H₂O)₂ → I^–(H₂O) + H₂O dissociation energy being more than 2 times larger than the (H₂O)₂ → 2H₂O dissociation energy, giving rise to highly mobile H₂O molecules near the I^–(H₂O)₂ dissociation threshold. This work illustrates the importance of treating anharmonicity correctly in unimolecular rate constant calculations

Chemical Dynamics Simulations of Intermolecular Energy Transfer: Azulene + N₂ Collisions

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 ⟨Δ<i>E</i>_c⟩ was obtained for Az* as it is collisionally relaxed. By comparing ⟨Δ<i>E</i>_c⟩ versus the bath density, the single collision limiting density was found for energy transfer. The resulting ⟨Δ<i>E</i>_c⟩, 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