Dynamic perturbation, description

The next three chapters deal with the most widely used classes of methods free energy perturbation (FEP) [3], methods based on probability distributions and histograms, and thermodynamic integration (TI) [1, 2], These chapters represent a mix of traditional material that has already been well covered, as well as the description of new techniques that have been developed only recendy. The common thread followed here is that different methods share the same underlying principles. Chapter 5 is dedicated to a relatively new class of methods, based on calculating free energies from nonequilibrium dynamics. In Chap. 6, we discuss an important topic that has not received, so far, sufficient attention - the analysis of errors in free energy calculations, especially those based on perturbative and nonequilibrium approaches. 

Due to the size of the variational problem, a large Cl is usually not a practicable method for recovering dynamic correlation. Instead, one usually resorts to some form of treatment based on many-body perturbation theory where an explicit calculation of all off-diagonal Cl matrix elements (and the diagonalization of the matrix) are avoided. For a detailed description of such methods, which is beyond the scope of this review, the reader is referred to appropriate textbooks295. For the present purpose, it suffices to mention two important aspects. 

To make an accurate FEP calculation, a good description of the system is required. This means that the parameters for the chosen force field must reproduce the dynamic behaviour of both species correctly. A realistic description of the environment, e.g. size of water box, and the treatment of the solute-solvent interaction energy is also required. The majority of the parameters can usually be taken from the standard atom types of a force field. The electrostatic description of the species at both ends of the perturbation is, however, the key to a good simulation of many systems. This is also the part that usually requires tailoring to the system of interest. Most force fields require atom centered charges obtained by fitting to the molecular electrostatic potential (MEP), usually over the van der Waals surface. Most authors in the studies discussed above used RHF/6-31G or higher methods to obtain the MEP. 

The statistical perturbation theory arising from the classical work of Zwanzig34 and its detailed implementation in a molecular dynamics program for computation of free energies is described in detail elsewhere.35 36 We give a very brief description of the method for the sake of completeness. The total Hamiltonian of a system may be written as the sum of the Hamiltonian (Ho) of the unperturbed system and the perturbation (Hi) ... 

The model of a reacting molecular crystal proposed by Luty and Eckhardt [315] is centered on the description of the collective response of the crystal to a local strain expressed by means of an elastic stress tensor. The local strain of mechanical origin is, for our purposes, produced by the pressure or by the chemical transformation of a molecule at site n. The mechanical perturbation field couples to the internal and external (translational and rotational) coordinates Q n) generating a non local response. The dynamical variable Q can include any set of coordinates of interest for the process under consideration. In the model the system Hamiltonian includes a single molecule term, the coupling between the molecular variables at different sites through a force constants matrix W, and a third term that takes into account the coupling to the dynamical variables of the operator of the local stress. In the linear approximation, the response of the system is expressed by a response function X to a local field that can be approximated by a mean field V ... 

A theoretical description of CC of excited state dynamics using pulse trains in the perturbative regime, as carried out in experiments [63-65], is presented in Ref. [35]. Analytical expressions relating the excited state populations to the pulse train control parameters are derived in Ref. [35] we refer therein for technical details. We focus on the results here. 

The highly excited and reactive dynamics, the details of which have been made accessible by recently developed experimental techniques, are characterized by transitions between classically regular and chaotic regimes. Now molecular spectroscopy has traditionally relied on perturbation expansions to characterize molecular energy spectra, but such expansions may not be valid if the corresponding classical dynamics turns out to be chaotic. This leads us to a reconsideration of such perturbation techniques and provides the starting point for our discussion. From there, we will proceed to discuss the Gutzwiller trace formula, which provides a semiclassical description of classically chaotic systems. 

Therefore, the simplest procedure to get the stochastic description of the reaction leads to the rather complicated set of equations containing phenomenological parameters / (equation (2.2.17)) with non-transparent physical meaning. Fluctuations are still considered as a result of the external perturbation. An advantage of this approach is a useful analogy of reaction kinetics and the physics of equilibrium critical phenomena. As is well known, because of their nonlinearity, equations (2.1.40) reveal non-equilibrium bifurcations [78, 113]. A description of diffusion-controlled reactions in terms of continuous Markov process - equation (2.2.15) - makes our problem very similar to the static and dynamic theory of critical phenomena [63, 87]. When approaching the bifurcation points, the systems with reactions become very sensitive to the environment fluctuations, which can even produce new nonequilibrium transitions [18, 67, 68, 90, 108]. The language developed in the physics of critical phenomena can be directly applied to the processes in spatially extended systems. 

Hamiltonian proposed by Muller and Plesset gives rise to a very successful and efficient method to treat electron correlation effects in systems that can be described by a single reference wave function. However, for a multireference wave function the Moller-Plesset division can no longer be made and an alternative choice of B(0> is needed. One such scheme is the Complete Active Space See-ond-Order Perturbation Theory (CASPT2) developed by Anderson and Roos [3, 4], We will briefly resume the most important definitions of the theory one is referred to the original articles for a more extensive description of the method. The reference wave function is a CASSCF wave function that accounts for the largest part of the non-dynamical electron correlation. The zeroth-order Hamiltonian is defined as follows and reduces to the Moller-Plesset operator in the limit of zero active orbitals ... 

The dynamics of reactions in solution must include an appropriate description of the solvent dynamics. To simplify this problem we start with some considerations supported by intuition and by some concepts described in the preceding sections. In the initial stages of the reaction the characteristic time is given by the nuclear motions of the solute, large enough to allow the use of the adiabatic perturbation approximation for the description of motions. In practice this means that the evolution of the system in time may be described with a time independent formalism, with the solvent reaction potential equilibrated at each time step for the appropriate geometry of the solute. 

The ASEP/MD method, acronym for Averaged Solvent Electrostatic Potential from Molecular Dynamics, is a theoretical method addressed at the study of solvent effects that is half-way between continuum and quantum mechanics/molecular mechanics (QM/MM) methods. As in continuum or Langevin dipole methods, the solvent perturbation is introduced into the molecular Hamiltonian through a continuous distribution function, i.e. the method uses the mean field approximation (MFA). However, this distribution function is obtained from simulations, i.e., as in QM/MM methods, ASEP/MD combines quantum mechanics (QM) in the description of the solute with molecular dynamics (MD) calculations in the description of the solvent. 

The computational and experimental analysis of time dependent solvatochromic shift in fluorescence spectra of solutes is used by Ladanyi to achieve an accurate description of solvation dynamics, i.e., the rate of solvent reorganization in response to a perturbation in solute-solvent interaction. 

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