Transition state dividing surfaces

The basic chemical description of rare events can be written in terms of a set of phenomenological equations of motion for the time dependence of the populations of the reactant and product species [6-9]. Suppose that we are interested in the dynamics of a conformational rearrangement in a small peptide. The concentration of reactant states at time t is N-n(t), and the concentration of product states is N-pU). We assume that we can define the reactants and products as distinct macrostates that are separated by a transition state dividing surface. The transition state surface is typically the location of a significant energy barrier (see Fig. 1). 

The original microscopic rate theory is the transition state theory (TST) [10-12]. This theory is based on two fundamental assumptions about the system dynamics. (1) There is a transition state dividing surface that separates the short-time intrastate dynamics from the long-time interstate dynamics. (2) Once the reactant gains sufficient energy in its reaction coordinate and crosses the transition state the system will lose energy and become deactivated product. That is, the reaction dynamics is activated crossing of the barrier, and every activated state will successfully react to fonn product. 

Given the foregoing assumptions, it is a simple matter to construct an expression for the transition state theory rate constant as the probability of (1) reaching the transition state dividing surface and (2) having a momenrnm along the reaction coordinate directed from reactant to product. Stated another way, is the equilibrium flux of reactant states across... 

The transition state theory rate constant can be constructed as follows. The total flux of trajectories across the transition state dividing surface will be equal to the rate of transition times the population of reactants at equilibrium N, or... 

In classical dynamics, the TST rate constant is the rate of one-way flux through the transition state dividing surface 9,11... 

For reactions with a well defined barrier the saddle point on the potential energy surface provides a good first approximation to the minimum energy configuration on the transition state dividing surface. Thus, in the quantum... 

The particular model used in the original simulation i- of this reaction was that of a Cl + CI2 like reaction as modeled by a LEPS potential energy surface. The barrier for this symmetric reaction was normally taken to be 20 kcal/mol (—33 kT at room temperature). Other simulations used 10 and 5 kcal/mol barriers. The reactants were placed in either a 50 or 100 atom solvent (Ar in the earliest simulations Ar, He, or Xe in the later work) with periodic truncated octahedron boundary conditions. To sample the rare reactive events, as described previously, this system was equilibrated with the Cl—Cl—Cl reaction coordinate constrained at its value at the transition state dividing surface (specifically, the value of the antisymmetric stretch coordinate was set equal to zero). From symmetry arguments, this constraint is the appropriate one (except in the rare case where the solvent stabilizes the transition state sufficiently such that a well is created at the top of the gas phase barrier). For each initial configuration, velocities were chosen for all coordinates from a Boltzmann distribution and molecular dynamics run for 1 ps both forward and backward in time. 

Pechukas and Pollak made a very important conceptual breakthrough by defining the classically optimum transition state dividing surface without reference to any particular set of reaction coordinates. That surface is called the PODS for periodic dividing surface. This approach can also be viewed as the best method to determine a coordinate system in which to apply adiabatic theory. ... 

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