Surface reaction path

Potential Surface Reaction Path Synthesis Spectral Matching Pipeline SilverScreen SPACFIL TUTSIM and FANSIM Windows WordPerfect ... 

Poulsen TD, M Garcia-Viloca, JL Gao, DG Truhlar (2003) Free energy surface, reaction paths, and kinetic isotope effect of short-chain Acyl-CoA dehydrogenase. J. Phys. Chem. B 107 (35) 9567-9578... 

While the assumption of only one type of surface sites for all adsorbants turned out to be an important factor in our results, assuming dissociative or non-dissociative adsorption did not change the results much. Obviously, under high temperature conditions, free surface sites do not play an important role in the surface reaction mechanism, while rather the competition for adsorbed oxygen appears to be the limiting factor for the different parallel surface reaction paths. 

Figure 6.16. The different surface reaction paths proposed for the synthesis of vinyl acetate.

Free Energy Surface, Reaction Paths, and Kinetic Isotope Effect of Short-Chain Acyl-CoA Dehydrogenase. 

In many cases, however, well-designed catalysts provide intrinsically different reaction paths, and the specific nature of the catalyst surface can be quite important. This is clearly the case with unimolecular reactions for which the surface concentration effect is not applicable. 

To calculate N (E-Eq), the non-torsional transitional modes have been treated as vibrations as well as rotations [26]. The fomier approach is invalid when the transitional mode s barrier for rotation is low, while the latter is inappropriate when the transitional mode is a vibration. Hamionic frequencies for the transitional modes may be obtained from a semi-empirical model [23] or by perfomiing an appropriate nomial mode analysis as a fiinction of the reaction path for the reaction s potential energy surface [26]. Semiclassical quantization may be used to detemiine anliamionic energy levels for die transitional modes [27]. 

Some fraction of such events will lead to the system remaining on the Odd surface until, further along the reaction path, the Odd surface again intersects the Even surface on the product side at which time quenching to produce ground-state products can occur. 

Molecular mechanics methods are not generally applicable to structures very far from equilibrium, such as transition structures. Calculations that use algebraic expressions to describe the reaction path and transition structure are usually semiclassical algorithms. These calculations use an energy expression fitted to an ah initio potential energy surface for that exact reaction, rather than using the same parameters for every molecule. Semiclassical calculations are discussed further in Chapter 19. 

Rather than using transition state theory or trajectory calculations, it is possible to use a statistical description of reactions to compute the rate constant. There are a number of techniques that can be considered variants of the statistical adiabatic channel model (SACM). This is, in essence, the examination of many possible reaction paths, none of which would necessarily be seen in a trajectory calculation. By examining paths that are easier to determine than the trajectory path and giving them statistical weights, the whole potential energy surface is accounted for and the rate constant can be computed. 

In the chapter on reaction rates, it was pointed out that the perfect description of a reaction would be a statistical average of all possible paths rather than just the minimum energy path. Furthermore, femtosecond spectroscopy experiments show that molecules vibrate in many dilferent directions until an energetically accessible reaction path is found. In order to examine these ideas computationally, the entire potential energy surface (PES) or an approximation to it must be computed. A PES is either a table of data or an analytic function, which gives the energy for any location of the nuclei comprising a chemical system. 

In the pure concerted reaction there is no need to invoke the cationic or anionic intermediates in describing the transition state, but it now becomes evident that some deviation from this idealized route may be possible, and then we need a way to comment upon and to measure the extent to which the cationic or anionic character is mixed in in the transition state. This is now widely accomplished with the aid of energy surfaces of the type shown schematically in Fig. 5-19. Depending on the nature of the surface, the reaction path may follow a route far from the diagonal representing the pure concerted reaction, and the primary goal is to identify the location of the transition state on this surface. 

Figure 5-19. Two-dimensional energy surface for generalized reaction R —> P showing the cationic fl i and anionic fl ) possible intermediates. The dashed line is the reaction path for the pure concerted reaction.

Theoretical predictions of potential energy surfaces and reaction paths can sometimes yield quite surprising results. In this section, we ll consider an example which illustrates the general approach toward and usefulness of studying potential energy surfaces in detail. 

An IRC calculation examines the reaction path leading down from a transition structure on a potential energy surface. Such a calculation starts at the saddle point and follows the path in both directions from the transition state, optimizing the geometry of the molecular system at each point along the path. In this way, an IRC calculation definitively connects two minima on the potential energy surface by a path which passes through the transition state between them. 

We ll now use Gaussian s reaction path following facility to explore the H CO potential energy surface. There are many minima on this surface—including... 

The entries in the table are arranged in order of increasing reaction coordinate or distance along the reaction path (the reaction coordinate is a composite variable spanning all of the degrees of freedom of the potential energy surface). The energy and optimized variable values are listed for each point (in this case, as Cartesian coordinates). The first and last entries correspond to the final points on each side of the reaction path. 

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