Transition State Levels Research Articles

Direct dynamics simulation of dioxetane formation and decomposition via the singlet ·O–O–CH2–CH2· biradical: Non-RRKM dynamics

Electronic structure calculations and direct chemical dynamics simulations are used to study the formation and decomposition of dioxetane on its ground state singlet potential energy surface. The stationary points for (1)O(2) + C(2)H(4), the singlet ·O-O-CH(2)-CH(2)· biradical, the transition state (TS) connecting this biradical with dioxetane, and the two transition states and gauche ·O-CH(2)-CH(2)-O· biradical connecting dioxetane with the formaldehyde product molecules are investigated at different levels of electronic structure theory including UB3LYP, UMP2, MRMP2, and CASSCF and a range of basis sets. The UB3LYP/6-31G∗ method was found to give representative energies for the reactive system and was used as a model for the simulations. UB3LYP∕6-31G∗ direct dynamics trajectories were initiated at the TS connecting the ·O-O-CH(2)-CH(2)· biradical and dioxetane by sampling the TS's vibrational energy levels, and rotational and reaction coordinate energies, with Boltzmann distributions at 300, 1000, and 1500 K. This corresponds to the transition state theory model for trajectories that pass the TS. The trajectories were directed randomly towards both the biradical and dioxetane. A small fraction of the trajectories directed towards the biradical recrossed the TS and formed dioxetane. The remainder formed (1)O(2) + C(2)H(4) and of these ∼ 40% went directly from the TS to (1)O(2) + C(2)H(4) without getting trapped and forming an intermediate in the ·O-O-CH(2)-CH(2)· biradical potential energy minimum, a non-statistical result. The dioxetane molecules which are formed dissociate to two formaldehyde molecules with a rate constant two orders of magnitude smaller than that predicted by Rice-Ramsperger-Kassel-Marcus theory. The reaction dynamics from dioxetane to the formaldehyde molecules do not follow the intrinsic reaction coordinate or involve trapping in the gauche ·O-CH(2)-CH(2)-O· biradical potential energy minimum. Important non-statistical dynamics are exhibited for this reactive system.

Theoretical and experimental determination of the effects governing the transannular Diels-Alder reaction of trans-trans-cis systems with or without activation of the dienophile.

A thorough study of the transannular Diels-Alder (TADA) reaction of trans-trans-cis macrocyclic trienes was carried out. It led to a better understanding of various parameters that govern the TADA reaction in particular and the Diels-Alder reaction in general. Thus, carbonyl activation of the dienophile and substitution of the diene are discussed, as well as the presence of substituents on the macrocycle and their respective effects at the transition-state level.

High-energy channeling in protein folding.

Recent controversy about the role of populated intermediates in protein folding emphasizes the need to better characterize other events on the folding pathway. A complication is that these involve high-energy states which are difficult to target experimentally since they do not accumulate kinetically. Here, we explore the energetics of high-energy states and map out the shape of the free-energy profile for folding of the two-state protein U1A. The analysis is based on nonlinearities in the GdnHCl dependence of the activation energy for unfolding, which we interpret in terms of structural changes of the protein-folding transition state. The result suggests that U1A folds by high-energy channeling where most of the conformational search takes place isoenergetically at transition-state level. This is manifested in a very broad and flat activation barrier, the top of which covers more than 60% of the reaction coordinate. The interpretation favors a folding mechanism where the pathway leading to the native protein is determined by the sequence's ability to stabilize productive transition states.

Electron transfer in mixed-valence biferrocenium salts: effect of zero-point energy difference and pronounced anion dependence

that the photoreaction is strongly inhibited in the en complex and that nonradiative decay to the ground state is a more effective competitor. Part of this rate inhibition in the en complex could arise prior to reverse intersystem crossing because the larger energy barrier for the activated route allows more competitive doublet nonradiative decay. However, the extent to which such decay can be accommodated is restricted by the observed linearity of the Arrhenius plot. At the transition-state level, other possible reasons are easy to imagine. If the transition state is seven-coordinate, then it may be more sterically crowded and have higher strain energy for the en complex than for the diammine. Alternatively, it may be that the required migration of the whole en ligand is a difficult and slow process so that deactivation and/or recoordination have a greater opportunity to compete. Finally, the diammine complex reactsz7 via a seven-coordinate species of microsecond lifetime. If the en complex behaves similarly, then its intermediate might be more likely to revert to starting material because of the bidentate nature of the leaving ligand. Concluding Remarks. We have presented evidence that after photochemical Cr-N bond breaking has occurred, it is possible for the reacting bidentate ligand to migrate from one coordination site to another in an edge displacement reaction. Since our proof relies on the assumption of stereochemical change, in the future additional evidence will be sought. It is fairly straightforward to design experiments with appropriate stereochemical sign-posting to prove group migration incontrovertably. Unfortunately, it is difficult to identify systems in which the starting compound can be prepared and unambiguously characterized and its photochemistry explored with product identification including stereochemistry. The work has shown, however, that complex ligand motions are likely and that further study of such phenomena is tractable and worth pursuing.