Transition solvation

For analysing equilibrium solvent effects on reaction rates it is connnon to use the thennodynamic fomuilation of TST and to relate observed solvent-mduced changes in the rate coefficient to variations in Gibbs free-energy differences between solvated reactant and transition states with respect to some reference state. Starting from the simple one-dimensional expression for the TST rate coefficient of a unimolecular reaction a— r... 

A number of types of calculations can be performed. These include optimization of geometry, transition structure optimization, frequency calculation, and IRC calculation. It is also possible to compute electronic excited states using the TDDFT method. Solvation effects can be included using the COSMO method. Electric fields and point charges may be included in the calculation. Relativistic density functional calculations can be run using the ZORA method or the Pauli Hamiltonian. The program authors recommend using the ZORA method. 

The HE, GVB, local MP2, and DFT methods are available, as well as local, gradient-corrected, and hybrid density functionals. The GVB-RCI (restricted configuration interaction) method is available to give correlation and correct bond dissociation with a minimum amount of CPU time. There is also a GVB-DFT calculation available, which is a GVB-SCF calculation with a post-SCF DFT calculation. In addition, GVB-MP2 calculations are possible. Geometry optimizations can be performed with constraints. Both quasi-Newton and QST transition structure finding algorithms are available, as well as the SCRF solvation method. 

This method has been applied to derive a multitude of paths for the coil-to-helix transition in polyalanine using a continuum solvation model [36]. 

Molecular dynamics simulations have also been used to interpret phase behavior of DNA as a function of temperature. From a series of simulations on a fully solvated DNA hex-amer duplex at temperatures ranging from 20 to 340 K, a glass transition was observed at 220-230 K in the dynamics of the DNA, as reflected in the RMS positional fluctuations of all the DNA atoms [88]. The effect was correlated with the number of hydrogen bonds between DNA and solvent, which had its maximum at the glass transition. Similar transitions have also been found in proteins. 

The electrostatic solvait effects discussed in the preceding paragraphs are not the only possible modes of interaction of solvent with reactants and transition states. Specific structural effects may cause either the reactants or the transition state to be particularly stroi ly solvated. Figure 4.12 shows how such solvation can affect the relative energies of the ground state and transition state and cause rate variations from solvent to solvent. 

Fig. 4.12. Potential energy liagrams showing effect of preferential solvation of transition state (a) and ground state (b) on the activation energy.

It should always be home in mind that solvent effects can modify the energy of both tile reactants and the transition slate. It is the difference in the two solvation effects that is the basis for changes in activation energies and reaction rates. Ihus, although it is conimon to express solvent effects solely in terms of reactant solvation or transition-slate solvation,... 

Fig. 4.14. Reactant and transition-state solvation in the reaction of ethyl acetate with hydroxide ion. [From P. Haberfield, J. Friedman, and M. F. Pinkson, J. Am. Chem. Soc. 94 71 (1972).]...

---