Excited-state reversible association–dissociation reaction: Renormalized kinetic theory in configuration space

Reversible Stochastically Gated Diffusion-Influenced Reactions

An approximate but accurate theory is developed for the kinetics of reversible binding of a ligand to a macromolecule when either can stochastically fluctuate between reactive and unreactive conformations. The theory is based on a set of reaction-diffusion equations for the deviations of the pair distributions from their bulk values. The concentrations are shown to satisfy non-Markovian rate equations with memory kernels that are obtained by solving an irreversible geminate (i.e., two-particle) problem. The relaxation to equilibrium is not exponential but rather a power law. In the Markovian limit, the theory reduces to a set of ordinary rate equations with renormalized rate constants.

Rate kernel theory for pseudo-first-order kinetics of diffusion-influenced reactions and application to fluorescence quenching kinetics

Theoretical foundation of rate kernel equation approaches for diffusion-influenced chemical reactions is presented and applied to explain the kinetics of fluorescence quenching reactions. A many-body master equation is constructed by introducing stochastic terms, which characterize the rates of chemical reactions, into the many-body Smoluchowski equation. A Langevin-type of memory equation for the density fields of reactants evolving under the influence of time-independent perturbation is derived. This equation should be useful in predicting the time evolution of reactant concentrations approaching the steady state attained by the perturbation as well as the steady-state concentrations. The dynamics of fluctuation occurring in equilibrium state can be predicted by the memory equation by turning the perturbation off and consequently may be useful in obtaining the linear response to a time-dependent perturbation. It is found that unimolecular decay processes including the time-independent perturbation can be incorporated into bimolecular reaction kinetics as a Laplace transform variable. As a result, a theory for bimolecular reactions along with the unimolecular process turned off is sufficient to predict overall reaction kinetics including the effects of unimolecular reactions and perturbation. As the present formulation is applied to steady-state kinetics of fluorescence quenching reactions, the exact relation between fluorophore concentrations and the intensity of excitation light is derived.

Fluorescence quenching by excimer formation: Quenching constant approximations for excimer formation-dissociation by classical potential models

Fluorescence quenching by excimer formation is studied on the assumption that the excimer formation and dissociation can be modeled as overdamped motion in an attractive potential (classical potential models). An approach to the zeroth-order, concentration-independent quenching constants is proposed which starts from a mean reaction-time ansatz and reduces the calculation essentially to the solution of the eigenvalue problem for the Smoluchowski operator which describes the excimer equilibration. For a square-well potential model it is shown that a quenching constant expansion in terms of relaxation modes, truncated at the kinetic level, gives a satisfactory approximation of the recently obtained exact zeroth-order result under defined conditions. It is demonstrated how this two-mode approach can be applied for a quenching constant estimation if the excimer formation and dissociation are modeled by more realistic interaction potentials, as for instance, Morse- or Gaussian-type ones.

Fluorescence quenching by reversible excimer formation: Kinetics and yield predictions for a classical potential association–dissociation model

Fluorescence quenching by reversible excimer formation is studied on the assumption that excimer formation and dissociation can be modelled as entering and leaving the attractive region of an monomer excited-monomer interaction potential by diffusion. To get some general insight in the kinetic consequences of such a type of modelling, the simple case of an attractive square-well potential is investigated. It is shown that three different kinetic regimes have to be distinguished: Two "reversible" ones in case of slow excimer radiative decay, in which the quenching kinetics can be formulated by Markovian or non-Markovian rate equations with both excimer formation and excimer dissociation terms, and an effectively "irreversible" regime if the excimer radiative decay is too rapid to allow the excimer equilibration. In the latter case a dissociation coefficient can no longer be defined and the quenching kinetics can only be predicted on the basis of generalized rate equations of a net-excimer-formation type. It is shown how the quenching constant formula must be generalized to be applicable in all kinetic situations.

Influence of diffusion on the kinetics of excited-state association–dissociation reactions: Comparison of theory and simulation

Several recent theories of the kinetics of diffusion influenced excited-state association--dissociation reactions are tested against accurate Brownian dynamics simulation results for a wide range of parameters. The theories include the relaxation time approximation (RTA), multiparticle kernel decoupling approximations and the so-called kinetic theory. In the irreversible limit, none of these theories reduce to the Smoluchowski result. For the pseudo-first-order target problem, we show how the RTA can be modified so that the resulting formalism does reduce correctly in the irreversible limit. We call this the unified Smoluchowski approximation, because it unites modern theories of reversible reactions with Smoluchowski's theory of irreversible reactions.