Vibrational transition state theory

Examining transition state theory, one notes that the assumptions of Maxwell-Boltzmann statistics are not completely correct because some of the molecules reaching the activation energy will react, lose excess vibrational energy, and not be able to go back to reactants. Also, some molecules that have reacted may go back to reactants again. 

According to the transition state theory, the pre-exponential factor A is related to the frequency at which the reactants arrange into an adequate configuration for reaction to occur. For an homolytic bond scission, A is the vibrational frequency of the reacting bond along the reaction coordinates, which is of the order of 1013 to 1014 s 1. In reaction theory, this frequency is diffusion dependent, and therefore, should be inversely proportional to the medium viscosity. Also, since the applied stress deforms the valence geometry and changes the force constants, it is expected... 

According to the quantum transition state theory [108], and ignoring damping, at a temperature T h(S) /Inks — a/ i )To/2n, the wall motion will typically be classically activated. This temperature lies within the plateau in thermal conductivity [19]. This estimate will be lowered if damping, which becomes considerable also at these temperatures, is included in the treatment. Indeed, as shown later in this section, interaction with phonons results in the usual phenomena of frequency shift and level broadening in an internal resonance. Also, activated motion necessarily implies that the system is multilevel. While a complete characterization of all the states does not seem realistic at present, we can extract at least the spectrum of their important subset, namely, those that correspond to the vibrational excitations of the mosaic, whose spectraFspatial density will turn out to be sufficiently high to account for the existence of the boson peak. 

Because the frequency of a weakly bonded vibrating system is relatively small, i.e. kBT hu we may approximate its partition function by the classical limit k T/hv, and arrive at the rate expression in transition state theory ... 

Hence, according to the transition state theory, adsorption becomes more likely if the molecule in the mobile physisorbed precursor state retains its freedom to rotate and vibrate as it did in the gas phase. Of course, this situation corresponds to minimal entropy loss in the adsorption process. In general, the transition from the gas phase into confinement in two dimensions will always be associated with a loss in entropy and the sticking coefficient is normally smaller than unity. 

It can be difficult to estimate theoretically the bond lengths and vibrational frequencies for the activated complex and the energy barrier for its formation. It is of interest to assess how the uncertainty in these parameters affect the rate constant predicted from transition state theory (TST). For the exchange reaction... 

Transition state theory, as embodied in Eq. 10.3, or implicitly in Arrhenius theory, is inherently semiclassical. Quantum mechanics plays a role only in consideration of the quantized nature of molecular vibrations, etc., in a statistical fashion. But, a critical assumption is that only those molecules with energies exceeding that of the transition state barrier may undergo reaction. In reality, however, the quantum nature of the nuclei themselves permits reaction by some fraction of molecules possessing less than the energy required to surmount the barrier. This phenomenon forms the basis for QMT. ... 

Transition state theory tells us that when a molecule of substrate has enough energy to jump the barrier, its structure is intermediate between that of the substrate and that of the product. Some bonds are stretched, partially broken, partially formed, and so forth. The arrangement of atoms that has the highest energy between the substrate and product is called the transition state. Transition state theory assumes that the transition state doesn t exist for more than the time required for one bond vibration (about 10 15 s)—so the transition state really doesn t exist, but we can talk about it as if it did. The AG s of activation are always positive. The more positive, the slower. 

Vibrational analysis has been carried out for each isotopomer transition state and the ku/ku values were calculated207 with the transition state theory approximation (equation 89)208-209 ... 

If hu0 is small compared with kT, the partition function becomes kT/hv0. The function kT/h which pre-multiplies the collision number in the transition state theory of the bimolecular collision reaction can therefore be described as resulting from vibration of frequency vq along the transition bond between the A and B atoms, and measures the time between each potential transition from reactants to product which will only occur provided that the activation energy, AE°0 is available. 

Quantitative estimates of E are obtained the same way as for the collision theory, from measurements, or from quantum mechanical calculations, or by comparison with known systems. Quantitative estimates of the A factor require the use of statistical mechanics, the subject that provides the link between thermodynamic properties, such as heat capacities and entropy, and molecular properties (bond lengths, vibrational frequencies, etc.). The transition state theory was originally formulated using statistical mechanics. The following treatment of this advanced subject indicates how such estimates of rate constants are made. For more detailed discussion, see Steinfeld et al. (1989). 

The transition state theory of reaction rates [21] provides the link between macroscopic reaction rates and molecular properties of the reactants, such as translational, vibrational, and rotational degrees of freedom. For an extensive discussion of transition state theory applied to surface reactions we refer to books by Zhdanov [25] and by Van Santen and Niemantsverdriet [27]. The desorption of a molecule M proceeds as follows ... 

Vibrational frequencies for various normal modes must be estimated and active as well as inactive energies should be decided. Numerical methods may be used to calculate rate constant k at various concentrations obtained by RRKM theory. The rate constant has been found to be same as given by conventional transition state theory, i.e. 

The kinetic model for proton transfer based upon transition state theory that incorporates a tunneling contribution to the overall reaction rate assumes that tunneling occurs near the region of the transition state (pathway a in Scheme 2.5). There is, however, another possibility for the reaction path for proton transfer. In lieu of thermally activating the vibration associated with the proton-transfer coordinate to bring it into the region of the transition state, the proton may instead... 

The rate constant ka(E) of Equation 14.3 is the rate constant which is calculated by transition state theory. Analogously to the discussion in Chapter 4 of conventional transition state theory, where chemical equilibrium is between reactants and transition state, it will be assumed here that an equilibrium exists between A (excited A molecules with vibrational energy E, equal to or larger than Eo, the minimum... 

As in the conventional transition state theory Equation 14.27 does not contain any reference to the mass of the reaction coordinate motion or to the length l of the transition state. While some aspects of the derivation have been skipped, it is hoped that the reader understands that the expression in the numerator for the sum of the vibrational energy levels in the transition state arises from Equation 14.25 which applies to the transition state but not to the excited molecule A. ... 

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