Trajectory calculations, reaction path

Both molecular dynamics studies and femtosecond laser spectroscopy results show that molecules with a sufficient amount of energy to react often vibrate until the nuclei follow a path that leads to the reaction coordinate. Dynamical calculations, called trajectory calculations, are an application of the molecular dynamics method that can be performed at semiempirical or ah initio levels of theory. See Chapter 19 for further details. 

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. 

The macmolplt graphics package is designed for displaying the output of GAMESS calculations. It can display molecular structures, including an animation of reaction-path trajectories. It also may be used to visualize properties, such as the electron density, orbitals, and electrostatic potential in two or three dimensions. 

It has been shown that there is a two-dimensional cut of the PES such that the MEP lies completely within it. The coordinates in this cut are 4, and a linear combination of qs-q-j. This cut is presented in fig. 64, along with the MEP. Motion along the reaction path is adiabatic with respect to the fast coordinates q -q and nonadiabatic in the space of the slow coordinates q -qi-Nevertheless, since the MEP has a small curvature, the deviation of the extremal trajectory from it is small. This small curvature approximation has been intensively used earlier [Skodje et al. 1981 Truhlar et al. 1982], in particular for calculating tunneling splittings in (HF)2- The rate constant of reaction (6.45a) found in this way is characterized by the values T<. = 20-25 K, = 10 -10 s , = 1-4 kcal/mol above T, which compare well with the experiment. 

The Rearrangement of 1,2,6-Heptatriene. The experimental facts and basic mechanistic idea behind this reaction were outlined in section 1.2. The molecular dynamics study began with a single CASSCF(8,8)/6-31G(d) trajectory started from TSl (see Fig. 21.2) with no kinetic energy (not even ZPE) in any of the real-frequency normal modes. The purpose of such an unphysical trajectory calculation is to see what is the steepest descent path down from the transition state... 

Let us consider first the in vacuo cases. Dynamical aspects of the reaction in vacuo may be recovered by resorting to calculations of semiclassical trajectories. A cluster of independent representative points, with accurately selected classical initial conditions, are allowed to perform trajectories according to classical mechanics. The reaction path, which is a static semiclassical concept (the best path for a representative point with infinitely slow motion), is replaced by descriptions of the density of trajectories. A widely employed approach to obtain dynamical information (reaction rate coefficients) is based on modern versions of the Transition State Theory (TST) whose original formulation dates back to 1935. Much work has been done to extend and refine the original TST. 

A question of great interest in the kinetics of reactions with cluster wells along the reaction path is the accuracy of transition state theory. Some classical trajectory calculations have indicated the possibility of large breakdowns (Cho et al. 1992), but these potential errors may be overestimated by the classical mechanical method employed, as discussed elsewhere (Truhlar et al. 1992 Wladkowski et al. 1992). 

Table XXIII displays the rate constants obtained from the MRRKM theory and the reaction path analysis. It is seen that the former are about a factor of two smaller, and the latter about a factor of two larger, than those derived from direct trajectory calculations. We infer that, since both the RRKM and the MRRKM calculated rate constants are smaller than that calculated from trajectory calculations, there is a nonstatistical contribution to the isomerization rate that is not captured by the MRRKM theory.

The comparison between the MRRKM and reaction-path rate constants and the rate constants obtained from trajectory calculations is subject to the... 

Trim-ethylene is a moiety with a shallow potential energy well on the reaction path connecting cyclopropane and propylene. Its very short unimolecular lifetime, following different types of initial excitations, has been calculated from classical trajectories [343,344] and compared with both experiment [391] and quantum dynamics [392]. Excellent agreement is found. This is an example of a rather large molecule, for which classical mechanics accurately describes the unimolecular dissociation because of the shallow potential energy minimum and, thus, very short lifetime. 

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