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Given a chemical reaction going from reactant (R) to the product (P) on a potential energy surface (PES) and a collective variable (CV) that discriminates between R and P, one can define a free-energy profile (FEP) as the logarithm of the marginal Boltzmann distribution of the CV. The FEP is not a true free energy, however, it is common to treat the FEP as the free-energy analog of the minimum energy path on the PES and to take the activation free energy, $ΔF^\ddagger_\mathrm{RP}$, as the difference between the maximum of the FEP at the transition state and the minimum at R. We show that this approximation can result in large errors. Since the FEP depends on the CV, it is therefore not unique, and different, discriminating CVs can yield different activation free energies for the same reaction. We derive an exact expression for the activation free energy that avoids this ambiguity with respect to the choice of CV. We find $ΔF^\ddagger_\mathrm{RP}$ to be a combination of the probability of the system being in the reactant state, the probability density at the transition state surface, and the thermal de~Broglie wavelength associated with the transition from R to P. We then evaluate the activation free energies based on our formalism for simple analytic models and realistic chemical systems. The analytic models show that the widespread FEP-based approximation applies only at low temperatures for CVs for which the effective mass of the associated pseudo-particle is small. Most chemical reactions of practical interest involve polyatomic molecules with complex, high-dimensional PES that cannot be treated analytically and pose the added challenge of choosing a good CV, typically through heuristics. We study the influence of the choice of CV and find that, while the reaction free energy is largely unaffected, $ΔF^\ddagger_\mathrm{RP}$ is quite sensitive.