Sangyoub Lee

A dynamical theory of nonadiabatic proton and hydrogen atom transfer reaction rates in solution

Abstract A dynamical theory for the rate constant k of hydrogen atom and proton transfer reactions in solution is presented for the nonadiabatic limit, where reaction is dominated by tunneling. Coupling and splitting fluctuation effects arising from intramolecular vibrational and solvent fluctuations are included in the description. Limiting regime analytic results for k are presented for high and low temperature and for weak and strong solvation. Differences between proton and hydrogen atom transfers are indicated, as are the contrasts with electron transfer rates.

Kinetics of diffusion‐influenced bimolecular reactions in solution. I. General formalism and relaxation kinetics of fast reversible reactions

A general theoretical framework for treating the kinetics of diffusion‐influenced bimolecular reactions in solution is presented. It is based on a hierachy of phenomenological kinetic equations for the reduced distribution functions of reactant molecules. With this formalism, a perturbation series expression for the rate coefficient for irreversible reactions involving a long‐ranged sink function is derived. For a delta‐function sink, it reduces to that obtained previously by Northrup and Hynes [Chem. Phys. Lett. 54, 244 (1978)]. It is demonstrated that the correctness of the Smoluchowski’s expression for the rate coefficient in the low concentration limit results from a cancellation of errors. For diffusion‐influenced reversible reactions involving a delta‐function sink, explicit expressions for the time‐dependent forward and reverse rate coefficients are derived. Experimental data on the relaxation kinetics of the triiodide ion formation reaction are reinterpreted, and consideration of diffusion effects...

Nonadiabatic solvation model for SN2 reactions in polar solvents

An analytic theory for SN2 reactions in polar solvents in the nonadiabatic solvation limit is presented and used to interpret the computer simulation results of the preceding paper by Bergsma et al. The theory is based on the nonadiabatic solvation limit of previous studies by van der Zwan and Hynes and incorporates the solvent approximately but explicitly via a coordinate additional to the intrinsic reaction coordinate. Central results include: an explicit expression for the reaction transmission coefficient κ, the dependence of reaction probability on kinetic energy, the interpretation of κ in terms of nonequilibrium solvation entropy effects, and the deviation of the reaction coordinate from that assumed in the standard equilibrium solvation transition state theory view of the reaction.

Solution reaction path Hamiltonian for reactions in polar solvents. I. Formulation

The solution reaction path Hamiltonian (SRPH) developed in the previous paper is applied to model SN2 and ionic dissociation reactions in water solvent. The solution reaction paths are determined and show marked deviations from a standard equilibrium solvation picture. The impact of potential anharmonicities, reaction path curvature, and varying solvent mass on the rate constant is calculated via the variational transition state theory approach of I, and the deviations from harmonic van der Zwan–Hynes (ZH) theory are calculated. Typically only minor deviations from ZH theory are found. The reasons for this are discussed.

Critical assessment of the automated AutoDock as a new docking tool for virtual screening

A major problem in virtual screening concerns the accuracy of the binding free energy between a target protein and a putative ligand. Here we report an example supporting the outperformance of the AutoDock scoring function in virtual screening in comparison to the other popular docking programs. The original AutoDock program is in itself inefficient to be used in virtual screening because the grids of interaction energy have to be calculated for each putative ligand in chemical database. However, the automation of the AutoDock program with the potential grids defined in common for all putative ligands leads to more than twofold increase in the speed of virtual database screening. The utility of the automated AutoDock in virtual screening is further demonstrated by identifying the actual inhibitors of various target enzymes in chemical databases with accuracy higher than the other docking tools including DOCK and FlexX. These results exemplify the usefulness of the automated AutoDock as a new promising tool in structure‐based virtual screening. Proteins 2006.

Kinetic theory of bimolecular reactions in liquid. III. Reversible association–dissociation: A+B⇄C

A theoretical formalism based on the fully renormalized kinetic theory is applied to a diffusion-influenced pseudo-first order reaction kinetics of reversible association–dissociation A+B⇄C including unimolecular decay processes. Linear response of the system, initially at equilibrium, to a thermal perturbation is examined and a rate kernel equation for the reactant concentrations is derived. The rate kernel has a hierarchical structure and the propagator appeared in the kernel expression is truncated by a disconnected approximation. When the unimolecular reactions are turned off, the response of the system not only shows the long-time power law of t−3/2 but also displays the proper behavior over the whole time region in accordance with previous computer simulation results. Moreover, it is shown that the amplitude of the long-time behavior predicted by previous workers is modified by a certain correction factor P which contains dynamical correlation effects. In this way, many-body complication inherent to...

Kinetic theory of bimolecular reactions in liquid. I. Steady-state fluorescence quenching kinetics

A microscopic kinetic theory for steady-state fluorescence quenching reaction in liquid is formulated. Based on a linear reaction-Liouville equation for the distribution function in phase space, we derived a memory equation for the relaxation of singlet density function of reactants by use of Mori’s projection operator technique. The expression of the memory kernel is analyzed by the fully renormalized kinetic theory developed by Mazenko. The memory kernel includes the many-body information via a hierarchical structure of a propagator in that. This hierarchy is truncated by a disconnected approximation for the propagator governing the dynamics of an orthogonalized doublet field creating their initial correlation via a bimolecular interaction. This approximation is different from the dynamic superposition approximation for reduced distribution functions made in usual hierarchical approaches. As a result, the detailed description of reactant dynamics becomes available and the memory kernel consists of a geo...

Nonequilibrium distribution function formalism for diffusion-influenced bimolecular reactions: Beyond the superposition approximation

We introduce an improved and systematic procedure for solving the diffusion-influenced reaction kinetics problem based on a hierarchical set of kinetic equations for many-particle distribution functions. As a representative example, we apply the formalism to the reversible association kinetics problem. The new method gives an approximate analytic solution which is in almost perfect agreement with the Brownian dynamics simulation results for the whole time range. It is shown that results of previous nonequilibrium distribution function theories are reproduced as lower order solutions in the present formalism.

Relations among the modern theories of diffusion-influenced reactions. II. Reduced distribution function theory versus modified integral encounter theory

It is shown that exactly the same results of the modified integral encounter theory (MET) of diffusion-influenced reactions can be derived from the nonequilibrium reduced distribution function (RDF) theory. The method of solution of the RDF theory is much simpler than that of the MET, and shows clearly that the sophisticated approximation scheme employed in the latter is effectively equivalent to a simple truncation approximation adopted in the former. We evaluate the relative accuracy of the various theories by comparing the theoretical results with the results of an accurate Brownian dynamics simulation and the exact theory that are available for simple reaction models.

Relations among the modern theories of diffusion-influenced reactions. I. Reduced distribution function theory versus memory function theory of Yang, Lee, and Shin

It is shown that exactly the same results of the memory function theory of diffusion-influenced reactions, presented by Yang, Lee, and Shin, can be derived from the nonequilibrium reduced distribution function (RDF) theory. Instead of the usual dynamic superposition approximation (SA), which has been widely used to truncate the hierarchy of RDF evolution equations, we introduce another type of truncation approximation. The new approximation provides simple analytic solutions that are in better agreement with the computer simulation and the known exact results than those obtained with the SA.