Langevin equation solvent effects

Langevin dynamics simulates the effect of molecular collisions and the resulting dissipation of energy that occur in real solvents, without explicitly including solvent molecules. This is accomplished by adding a random force (to model the effect of collisions) and a frictional force (to model dissipative losses) to each atom at each time step. Mathematically, this is expressed by the Langevin equation of motion (compare to Equation (22) in the previous chapter) ... 

Langevin dynamics a technique to reduce the total number of equations of motion that are solved. Utilize the Coupled Heat Bath, wherein the method models the solvent effect by incorporating a friction constant into the overall expression for the force. 

In the previous chapter we considered a rather simple solvent model, treating each solvent molecule as a Langevin-type dipole. Although this model represents the key solvent effects, it is important to examine more realistic models that include explicitly all the solvent atoms. In principle, we should adopt a model where both the solvent and the solute atoms are treated quantum mechanically. Such a model, however, is entirely impractical for studying large molecules in solution. Furthermore, we are interested here in the effect of the solvent on the solute potential surface and not in quantum mechanical effects of the pure solvent. Fortunately, the contributions to the Born-Oppenheimer potential surface that describe the solvent-solvent and solute-solvent interactions can be approximated by some type of analytical potential functions (rather than by the actual solution of the Schrodinger equation for the entire solute-solvent system). For example, the simplest way to describe the potential surface of a collection of water molecules is to represent it as a sum of two-body interactions (the interac-... 

Many solvents do not possess the simple structure that allows their effects to be modeled by the Langevin equation or generalized Langevin equation used earlier to calculate the TS trajectory [58, 111, 112]. Instead, they must be described in atomistic detail if their effects on the effective free energies (i.e., the time-independent properties) and the solvent response (i.e., the nonequilibrium or time-dependent properties) associated with the... 

The Langevin equation, Eq. (11.5), that was used in Kramers calculation of the dynamical effects on the rate constant, is only valid in the limit of long times, where an equilibrium situation may be established. The reaction coordinate undergoes many collisions with the atoms in the solvent due to thermal agitation. From the Langevin equation of motion and Eq. (11.9), we obtained an expression for the autocorrelation function of the velocity ... 

In this equation g(t) represents the retarded effect of the frictional force, and /(f) is an external force including the random force from the solvent molecules. We see, in contrast to the simple Langevin equation with a constant friction coefficient, that the friction force at a given time t depends on all previous velocities along the trajectory. The friction force is no longer local in time and does not depend on the current velocity alone. The time-dependent friction coefficient is therefore also referred to as a memory kernel . A short-time expansion of the velocity correlation function based on the GLE gives (fcfiT/M)( 1 — (g/M)t2/(2r) + ), where r is the decay time of g(t), and it therefore does not have a discontinuous first derivative at t = 0. The discussion of the properties of the GLE is most easily accomplished by using so-called linear response theory, which forms the theoretical basis for the equation and is a powerful method that allows us to determine non-equilibrium transport coefficients from equilibrium properties of the systems. A discussion of this is, however, beyond the scope of this book. 

Dynamic medium effects in solution kinetics were first recognized by Kramers [41], He treated the problem on the basis of the Langevin equation [42] according to which the velocity of the reactants along the reaction coordinate and the friction of the surrounding medium play a role. Details of Kramers theory are not given here but an introduction to this subject can be found elsewhere [G3], The parameters involved in quantitatively assessing the dynamic solvent effect are the frequency associated with the shape of the barrier of the transition state and a friction parameter which is related to solvent viscosity. 

Static medium effects appear in equation (7.10.6) through Vr and A G°, both of which depend on solvent properties. After solving the Langevin equation, the following expression is obtained for Kj ... 

All of the simulation approaches, other than harmonic dynamics, include the basic elements that we have outlined. They differ in the equations of motion that are solved (Newton s equations, Langevin equations, etc.), the specific treatment of the solvent, and/or the procedures used to take account of the time scale associated with a particular process of interest (molecular dynamics, activated dynamics, etc.). For example, the first application of molecular dynamics to proteins considered the molecule in vacuum.15 These calculations, while ignoring solvent effects, provided key insights into the important role of flexibility in biological function. Many of the results described in Chapts. VI-VIII were obtained from such vacuum simulations. Because of the importance of the solvent to the structure and other properties of biomolecules, much effort is now concentrated on systems in which the macromolecule is surrounded by solvent or other many-body environments, such as a crystal. 

To treat the effects of solvent in a simple fashion, the Langevin equation... 

Stochastic dynamics The stochastic dynamics (SD) method is a further extension of the original molecular dynamics method. A space-time trajectory of a molecular system is generated by integration of the stochastic Langevin equation which differs from the simple molecular dynamics equation by the addition of a stochastic force R and a frictional force proportional to a friction coefficient g. The SD approach is useful for the description of slow processes such as diffusion, the simulation of electrolyte solutions, and various solvent effects. 

The authors proceed to calculate the reaction rates by the flux correlation method. They find that the molecular dynamics results are well described by the Grote-Hynes theory [221] of activated reactions in solutions, which is based on the generalized Langevin equation, but that the simpler Kramers model [222] is inadequate and overestimates the solvent effect. Quite expectedly, the observed deviations from transition state theory increase with increasing values of T. 

The pseudo-Liouville operator does couple these doublet fields to triplet fields such as 8 abs cds involving the solvent molecules. Thus one of the simplest forms for the pair kinetic equation can be obtained by explicitly including doublet and triplet fields in the generalized Langevin equation. This procedure yields a treatment of the effects of solvent dynamics on the motion of the reactive pair that is much more sophisticated than that given in the singlet kinetic equation discussed in the preceding... 

No calculations yet have tackled this problem in all its complexity. Typically, it is assumed that the photodissociation produces some initial distribution of pairs, and then the subsequent time evolution of the unreacted pair probability is calculated. Even this more modest program has been carried out only at the diffusion and Langevin equation levels. We briefly comment on these results, since they indicate the magnitude of the solvent and velocity relaxation effects. 

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