But such processes often occur on time-scales that are beyond the scope of current molecular dynamics simulations (> micro-second). However, they can be simulated when the end-states of the reaction are available or can be defined.
I have coined the term Molecular Kinematics to refer to a time-independent description of such reactions in terms of its essential motions along the minimum energy path, yielding the transition state(s) and the corresponding activation barrier(s).
I have designed a method to find such minimum energy paths in macromolecules, called Conjugate Peak Refinement (Chem. Phys. Lett. 1992, vol. 194, p. 252). This method is being applied to various reactions and conformational transitions proteins (see research-page).
New methods for computing the free energy along a minimum energy path are also being developped. The energy barrier yields the enthalpic component of the free energy barrier characterizing the process. The entropic component may then be computed from normal-mode calculations (Fischer et al., J. Phys. Chem. 1998) or from free-energy perturbation methods (Neria, Fischer & Karplus, J. Chem. Physics 1996). From these thermodynamic quantities, the reaction rate can be derived and compared with the experimentally measured rate.
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