Reaction coordinate identification

This is an interesting exercise, but we should not become excessively concerned with formal schemes for the identification of the rds. We want to know the rds because it is a piece of information about the reaction mechanism. If we have already acquired so much information about the system that we can construct a reaction coordinate diagram displaying ail intermediates and transition states, we probably have no need to specify the rds. As an example of the experimental detection of the rds we will describe Jencks study of the reaction of hydroxyiamine with acetone. The overall reaction is... 

The overall objective of these studies is to unravel mechanisms of interfacial PT. This requires identification of collective coordinates (or reaction coordinates) and transition pathways of transferring protons. Differences in activation energies and rates of corresponding mechanism due to distinct polymer constituents, acid head groups, side chain lengths, side chain densities, and levels of hydration have to be examined. Comparison with experimental... 

Microscopic models of electron transfer processes aim to provide a connection between the nature of the system and the electron transfer event that is lacking in BV. This enables us to rationalize experimental data in terms of the molecular properties of the system as well as to make predictions. Such approaches include first-principles basis for the calculation of the corresponding energy surface and the identification of the fundamental factors behind the activation barrier and the meaning of the reaction coordinate. 

As we have discussed in depth elsewhere, despite the similarities in the structures of hypericin and hypocrellin, which are centered about the perylene quinone nucleus, their excited-state photophysics exhibit rich and varied behavior. The H-atom transfer is characterized by a wide range of time constants, which in certain cases exhibit deuterium isotope effects and solvent dependence. Of particular interest is that the shortest time constant we have observed for the H-atom transfer is 10 ps. This is exceptionally long for such a process, 100 fs being expected when the solute H atom does not hydrogen bond to the solvent [62]. That the transfer time is so long in the perylene quinones has been attributed to the identification of the reaction coordinate with skeletal motions of the molecule [48, 50]. 

It must be remembered, furthermore, that the identification of the H-atom translocation mode is not equivalent to the identification of the reaction coordinate. We have attributed the absence of a deuterium isotope effect on the excited-state H-atom transfer (for the 10-ps component in hypericin and hypo-crellin A) to the zero-point energy in the proton coordinate lying above the barrier, with the H-atom being effectively delocalized between the two oxygen atoms. Consequently, the reaction coordinate for the excited-state H-atom transfer cannot be identified with the proton coordinate, and it must be concluded that other intramolecular motions are in fact responsible for the process. Temperature-dependent measurements indicate that these motions are extremely low amplitude, Ea 0.05 kcal/mol for hypericin [37]. Because the nature of this motion is not yet identified, we refer to it as the skeleton coordinate [48, 71, 82]. We propose that it is the time scale for this latter conformational change... 

We can immediately draw important conclusions about molecular stability from Figure 2.2, and the identification of It] with the HOMO-LUMO energy gap. Soft molecules will be less stable than similar hard molecules. They will dissociate or isomerize more readily. In the perturbation theory of such reactions, change occurs by mixing in excited-state wave functions with the ground-state wave function. If Q is the reaction coordinate,... 

The results of these experiments form a picture of the dominant features of the methane-nickel surface interaction potential that control the mechanism of the dissociation of methane. We will find that there is indeed a barrier to the dissociative chemisorption of methane and that translational and vibrational energy of the incident methane molecule are effective in overcoming 1t. The identification of this barrier along the dissociative reaction coordinate allows the establishment of a link between low pressure, ultrahigh vacuum surface science and high pressure catalysis (ref. 3). 

Analysis of the frequencies along the minimum energy path allows identification of the modes that are most strongly coupled to the reaction coordinate and have the largest participation in the tunneling process. Figure 27.9 shows all 32... 

One of the first approaches introduced and used in condensed phases, also in the sense of the historical development, was a biasing technique known as the Blue Moon [55]. This approach was better refined over the years [56] to become more user-friendly and easily implementable in a computer code. For all the details, we refer the reader to the cited original publications. Just to summarize the essential points, let us recall that in the case of first principles dynamical simulation, the method relies on the identification of a reaction coordinate, or order parameter, = (R/) of a given subset of atomic coordinates (Lagrangean variables) R/ able to track the activated process or chemical reaction on which one wants to focus. The simplest example is represented by the distance = R/—Ry between two atoms that are expected to form or break a chemical bond. This analytical function is added to, e.g., a Car-Parrinello Lagrangean as a holonomic constraint. 

D. A. C. Beck and V. Daggett, Biophys. /., 93, 3382 (2007). A One-Dimensional Reaction Coordinate for Identification of Transition States from Explicit Solvent P(fold)-Like Calculations. 

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