Chemical dynamics trajectory simulations were used to study the atomic-level mechanisms of the OH
−
+ CH
3
F → CH
3
OH + F
−
S
N
2 nucleophilic substitution reaction. The reaction dynamics, from the [OH⋯CH
3
⋯F]
−
central barrier to the reaction products, are simulated by ab initio direct dynamics. The reaction's potential energy surface has a deep minimum in the product exit channel arising from the CH
3
OH⋯F
−
hydrogen-bonded complex. Statistical theories of unimolecular reaction rates assume that the reactive system becomes trapped in this minimum and forms an intermediate, with random redistribution of its vibrational energy, but the majority of the trajectories (90%) avoided this potential energy minimum and instead dissociated directly to products. This finding is discussed in terms of intramolecular vibrational energy redistribution (IVR) and the relation between IVR and molecular structure. The finding of this study may be applicable to other reactive systems where there is a hierarchy of time scales for intramolecular motions and thus inefficient IVR.
A new series of stable, unsymmetrical squaraine near-IR sensitizers (JK-216 and JK-217), which are assembled using both thiophenyl pyrrolyl and indolium groups, exhibit a panchromatic light harvesting up to 780 nm. The JK-216 based cell exhibited a record efficiency of 6.29% for near-IR DSSCs. In addition, the JK-217 device showed an excellent stability under a light soaking test at 60 °C for 1000 h.
Quasiclassical direct dynamics trajectories, calculated at the MP2/6-31G level of theory, are used to study the central barrier dynamics for the C1(-) + CH(3)Cl S(N)2 reaction. Extensive recrossings of the central barrier are observed in the trajectories. The dynamics of the Cl(-)-CH(3)Cl complex is non-RRKM and transition state theory (TST) is predicted to be an inaccurate model for calculating the Cl(-) + CH(3)Cl S(N)2 rate constant. Direct dynamics trajectories also show that Cl(-) + CH(3)Cl trajectories, which collide backside along the S(N)2 reaction path, do not form the Cl(-)-CH(3)Cl complex. This arises from weak coupling between the Cl(-)-CH(3)Cl intermolecular and CH(3)Cl intramolecular modes. The trajectory results are very similar to those of a previous trajectory study, based on a HF/6-31G* analytic potential energy function, which gives a less accurate representation of the central barrier region of the Cl(-) + CH(3)Cl reaction than does the MP2/6-31G* level of theory used here. Experiments are suggested for investigating the non-RRKM and non-TST dynamics predicted by the trajectories.
A QM ϩ MM direct chemical dynamics simulation was performed to study collisions of protonated octaglycine, gly 8 -H ϩ , with the diamond {111} surface at an initial collision energy E i of 100 eV and incident angle i of 0°and 45°. The semiempirical model AM1 was used for the gly 8 -H ϩ intramolecular potential, so that its fragmentation could be studied. Shattering dominates gly 8 -H ϩ fragmentation at i ϭ 0°, with 78% of the ions dissociating in this way. At i ϭ 45°shattering is much less important. For i ϭ 0°there are 304 different pathways, many related by their backbone cleavage patterns. For the i ϭ 0°fragmentations, 59% resulted from both a-x and b-y cleavages, while for i ϭ 45°70% of the fragmentations occurred with only a-x cleavage. For i ϭ 0°, the average percentage energy transfers to the internal degrees of freedom of the ion and the surface, and the energy remaining in ion translation are 45%, 26%, and 29%. For 45°these percentages are 26%, 12%, and 62%. The percentage energy-transfer to ⌬E int for i ϭ 0°is larger than that reported in previous experiments for collisions of des-Arg 1 -bradykinin with a diamond surface at the same i . This difference is discussed in terms of differences between the model diamond surface used in the simulations and the diamond surface prepared for the experiments. (J Am Soc Mass Spectrom 2009, 20, 939 -948)
A quantum mechanical and molecular mechanical (QM + MM) direct dynamics classical trajectory simulation is used to study energy transfer and fragmentation in the surface-induced dissociation (SID) of N-protonated diglycine, (gly)2H+. The peptide ion collides with the hydrogenated diamond [111] surface. The Austin Model 1 (AM1) semiempirical electronic structure theory is used for the (gly)2H+ intramolecular potential and molecular mechanical functions are used for the diamond surface potential and peptide/surface intermolecular potential. The simulations are performed at collision energies Ei of 30, 50, 70, and 100 eV and collision angle of 0 degrees (perpendicular to the surface). The percent energy transfer to the peptide ion is nearly independent of Ei, while energy transfer to the surface increases with increase in Ei. A smaller percent of the energy remains in peptide translation as Ei is increased. These trends in energy transfer are consistent with previous trajectory simulations of SID. At each Ei the most likely initial pathway leading to fragmentation is rupture of the +H3NCH2-CONHCH2COOH bond. Fragmentation occurs by two general mechanisms. One is the traditional Rice-Ramsperger-Kassel-Marcus (RRKM) model in which the peptide ion is activated by its collision with the surface, "bounces off", and then dissociates after undergoing intramolecular vibrational energy redistribution (IVR). The other mechanism is shattering in which the ion fragments as it collides with the surface. Shattering is the origin of the large increase in number of product channels with increase in Ei, i.e., 6 at 30 eV, but 59 at 100 eV. Shattering becomes the dominant dissociation mechanism at high Ei.
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