Partition functions in transition-state theory

By considering the symmetry of the normal modes of transition states Murrell and Laidler showed that problems encountered when calculating the statistical factors of transition states (which are needed to calculate the partition function in transition state theory) were associated with configurations of too high a symmetry to be transition states (61, 62). 

Finally, the generalization of the partition function in transition state theory (equation (A3.4.961) is given by... 

Anharmonicity for Bending Partition Functions in Transition-State Theory. 

B. C. Garrett and D. G. Truhlar, Importance of quartic anharmon-icity for bending partition functions in transition state theory, J. Phys. Chem. 83 1915 (1979). 

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 ... 

From the preceding paragraph, the reader will note that many assumptions are involved in transition-state theory. Alternative derivations exhibit differing hypotheses. In a quicker but perhaps less intuitive derivation, translation in the reaction coordinate is treated formally as the low-frequency limit of a vibrational mode. Expansion of the vibrational partition function given in Section A.2.3 then yields Q = Q (k T/hv), which is substituted into equation (A-24), to be used directly in equation (66), thereby producing equation (69) when v = 1/t. The decay time thus is identified as the reciprocal of the small frequency of vibration in the direction of the reaction coordinate. 

Entropy of activation (continued) sign of, 256 Entropy unit, 242 Enzyme catalysis, 102 Enzyme-substrate complex, 102 Equilibrium, 60, 97, 99, 105, 125, 136 condition for, 205 displacement from, 62, 78 in transition state theory, 201, 205 Equilibrium assumption, 96 Equilibrium constant, 61. 138 complexation, 152 dissociation, 402 ionization, 402 kinetic determination of, 279 partition functions in, 204 pressure dependence of, 144 temperature dependence of, 143, 257 transition state, 207 Equivalence, kinetic, 123 Error analysis, 40 Error propagation, 40 Ester hydrolysis, 4 Euler s method, 106 Excess acidity method, 451 Exchange... 

The expression for the transitional mode contribution to the canonical transition state partition function in flexible RRKM theory is particularly simple [200] ... 

Flexible RRKM theory and the reaction path Hamiltonian approach take two quite different perspectives in their evaluation of the transition state partition functions. In flexible RRKM theory the reaction coordinate is implicitly assumed to be that which is appropriate at infinite separation and one effectively considers perturbations from the energies of the separated fragments. In contrast, the reaction path Hamiltonian approach considers a perspective that is appropriate for the molecular complex. Furthermore, the reaction path Hamiltonian approach with normal mode vibrations emphasizes the local area of the potential along the minimum energy path, whereas flexible RRKM theory requires a global potential for the transitional modes. One might well imagine that each of these perspectives is more or less appropriate under various conditions. 

For the interpretation of experimental observations on ice the microscopic picture of the diffusion process is established through the evaluation of atomic jump rates. In transition state theory the atomic jump lattempt frequency appears as a ratio of two partition functions of which the numerator involves the potential at the saddle point on top of the potential ridge, through which all jump trajectories in configuration space must cross. The Vineyard theory approximates the relevant potential surfaces harmonically described. Using this transition state theory we can find the jump rate of a particular protons as follows ... 

These equations lead to fomis for the thermal rate constants that are perfectly similar to transition state theory, although the computations of the partition functions are different in detail. As described in figrne A3.4.7 various levels of the theory can be derived by successive approximations in this general state-selected fomr of the transition state theory in the framework of the statistical adiabatic chaimel model. We refer to the literature cited in the diagram for details. 

This is connnonly known as the transition state theory approximation to the rate constant. Note that all one needs to do to evaluate (A3.11.187) is to detennine the partition function of the reagents and transition state, which is a problem in statistical mechanics rather than dynamics. This makes transition state theory a very usefiil approach for many applications. However, what is left out are two potentially important effects, tiiimelling and barrier recrossing, bodi of which lead to CRTs that differ from the sum of step frmctions assumed in (A3.11.1831. 

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. 

The rate of reaction from transition state theory is given by equation (4.31) as Rate of reaction = A v Therefore, in terms of partition function... 

Transition state theory in terms of partition function)... 

In earlier sections of this chapter we learned that the calculation of isotope effects on equilibrium constants of isotope exchange reactions as well as isotope effects on rate constants using transition state theory, TST, requires the evaluation of reduced isotopic partition function ratios, RPFR s, for ordinary molecular species, and for transition states. Since the procedure for transition states is basically the same as that for normal molecular species, it is the former which will be discussed first. 

Of course, one is not really interested in classical mechanical calculations. Thus in normal practice the partition functions used in TST, as discussed in Chapter 4, are evaluated using quantum partition functions for harmonic frequencies (extension to anharmonicity is straightforward). On the other hand rotations and translations are handled classically both in TST and in VTST, which is a standard approximation except at very low temperatures. Later, by introducing canonical partition functions one can direct the discussion towards canonical variational transition state theory (CVTST) where the statistical mechanics involves ensembles defined in terms of temperature and volume. There is also a form of variational transition state theory based on microcanonical ensembles referred to by the symbol p,. Discussion of VTST based on microcanonical ensembles pVTST is beyond the scope of the discussion here. It is only mentioned that in pVTST the dividing surface is... 

The use of transition state theory as a convenient expression of rate data is obviously complex owing to the presence of the temperature-dependent partition functions. Most researchers working in the area of chemical kinetic modeling have found it necessary to adopt a uniform means of expressing the temperature variation of rate data and consequently have adopted a modified Arrhenius form... 

The conversion of (kgT/h) to (co/it) may be derived within the Eyring Transition State Theory as due to the inclusion in the prefactor of the reactant vibrational (harmonic) partition function. 

The rate constants, k+ and k of the forward and backward reactions are finally derived from (12) and (13) according to the transition-state theory, i.e. assuming that the transition and the initial states, on the one hand, and the transition and final states, on the other, are in equilibrium (Glasstone et al., 1941). Thus, estimating the partition function of these three states in the classical way gives (18) and (19), where p is the reduced mass of the two reactants in the homogeneous case and m the mass of the reactant in the electrochemical case. 

Occasionally, the rates of bimolecular reactions are observed to exhibit negative temperature dependencies, i.e., their rates decrease with increasing temperature. This counterintuitive situation can be explained via the transition state theory for reactions with no activation energy harriers that is, preexponential terms can exhibit negative temperature dependencies for polyatomic reactions as a consequence of partition function considerations (see, for example, Table 5.2 in Moore and Pearson, 1981). However, another plausible explanation involves the formation of a bound intermediate complex (Fontijn and Zellner, 1983 Mozurkewich and Benson, 1984). To... 

Following Fey nman s original work, several authors pmsued extensions of the effective potential idea to construct variational approximations for the quantum partition function (see, e g., Refs. 7,8). The importance of the path centroid variable in quantum activated rate processes was also explored and revealed, which gave rise to path integral quantum transition state theory and even more general approaches. The Centroid Molecular Dynamics (CMD) method for quantum dynamics simulation was also formulated. In the CMD method, the position centroid evolves classically on the efiective centroid potential. Various analysis and numerical tests for realistic systems have shown that CMD captures the main quantum effects for several processes in condensed matter such as transport phenomena. 

Some important systems, which certainly do not fulfill the assumptions of harmonic transition state theory are gas phase reactions. In the gas phase, there are zero-modes such as translation and rotation, and these lead to totally different configuration integrals than those obtained from a normal mode analysis. For these species one can in a simple manner modify the terms going into the HTST rate by incorporating the molecular partition functions [3,119]. 

The Ufson-Roig matrix theory of the helix-coil transition In polyglycine is extended to situations where side-chain interactions (hydrophobic bonds) are present both In the helix and in the random coil. It is shown that the conditional probabilities of the occurrence of any number and size of hydrophobic pockets In the random coil can be adequately described by a 2x2 matrix. This is combined with the Ufson-Roig 3x3 matrix to produce a 4 x 4 matrix which represents all possible combinations of any amount and size sequence of a-helix with random coil containing all possible types of hydrophobic pockets In molecules of any given chain length. The total set of rules is 11) a state h preceded and followed by states h contributes a factor wo to the partition function 12) a state h preceded and followed by states c contributes a factor v to the partition function (3) a state h preceded or followed by one state c contributes a factor v to the partition function 14) a state c contributes a factor u to the partition function IS) a state d preceded by a state other than d contributes a factor s to the partition function 16) a state d preceded by a state d contributes a factor r to the partition function. 

It is known that the isotope effect may occur not only because of tunneling. Within the framework of the transition-state theory, which does not take tunneling into account, the isotope effect is explained by the variations of the energies of the ground vibrational levels and by the variations of the partition functions of the reagents and of the activated complex upon changing one isotope for another [53]. To make it clear to what extent the isotope effect in reactions (a) (d) is connected with tunneling, it is useful to mention... 

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