Free Energy Perturbation FEP

Free energy perturbation (FEP) theory is now widely used as a tool in computational chemistry and biochemistry [91]. It has been applied to detennine differences in the free energies of solvation of two solutes, free energy differences in confonnational or tautomeric fonns of the same solute by mutating one molecule or fonn into the other. Figure A2.3.20 illustrates this for the mutation of CFt OFl CFt CFt [92]. 

The ratio of the quantum partition functions (Eq. (4-29)) for two different isotopes can be obtained directly through free energy perturbation (FEP) theory by perturbing the mass from the light isotope to the heavy isotope. Consequently, only one simulation of a given isotopic reaction is performed, while the ratio of the partition function, i.e., the KIE, to a different isotopic reaction, is obtained by FEP. This is conceptually and practically an entirely different approach than that used previously [23]. 

In this chapter, we will examine in depth the characteristic errors of two free energy techniques and present improved methods based on a better understanding of their behavior. The two techniques examined are free energy perturbation (FEP) [2] and nonequilibrium work (NEW) based on Jarzynski s equality [3-6]. These techniques are discussed in Chaps. 2 and 5. The FEP method is one of the most popular approaches for computing free energy differences in molecular simulation see, e.g., [1, 7-10]. The recently developed NEW method, which is closely related to FEP, is gaining popularity in both simulation [11-18] and experimental applications [19-21],... 

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. 

Whilst this Chapter is primarily concerned with the methods of determining the free energies of tautomeric or ionisation equilibria via computer simulation of free energy differences, many of the issues raised relate also to the determination of other molecular properties upon which behaviour of the molecule within the body may depend, such as the redox potential or the partition coefficient.6 In the next section, we shall give a brief explanation of the methods used to calculate these free energy differences -namely the use of a thermodynamic cycle in conjunction with ab initio and free energy perturbation (FEP) methods. This enables an explicit representation of the solvent environment to be used. In depth descriptions of the various simulation protocols, or the accuracy limiting factors of the simulations and methods of validation, have not been included. These are... 

Table 7 compares free energies of hydration125 produced by the two types of solvent models that have been presented discrete molecular and continuum. The discrete molecular involved classical force field molecular dynamics (MD) and a free energy perturbation (FEP) technique whereby the solute molecule is annihilated to dummy atoms, so that absolute AGhydration are obtained the continuum were SCRF/PCM calculations, with Claverie-Pierotti Gcavilatlon and Floris-Tomasi Gvdw. The... 

For the three conformers, the binding sequence is Na > K > Rb > Cs. This is supported by energy component analysis on the trajectories, as well as by Free energy perturbation (FEP) calculations. Intrinsically, Cs+ has the weakest interactions with both hosts. The largest contribution of the cation/host interaction energy comes from the ether ring rather than from the aromatic moieties. Each complex displays a clear conformational preference. Sodium is most stable in the cone conformation, whereas cesium is most stable in the 1,3-altemate conformation. 

Thermodynamic cycles are used in MD simulations for computing accurate relative free energies. Free energy perturbation (FEP) calculations simulate the conversion of one molecule into another similar one (81,82). By... 

A review cataloging intramolecular Diels-Alder reactions as key steps in the total synthesis of natural products has been published.78 A key step in the total synthesis (g) of (+)-dihydrocompactin (66) is the intramolecular ionic Diels-Alder reaction of the trienone (63) to yield the (+)-compactin core compound (65) via the intermediate cyclic vinyloxocarbenium ion (64) (Scheme 17).79 The intramolecular Diels-Alder reaction of the Asp-Thr tethered compound (67) produced the cycloadduct (68) with high regio- and stereo-selectivity (Scheme 18).80 Mixed quantum and molec- (g) ular mechanics (QM/MM) combined with Monte Carlo simulations and free-energy perturbation (FEP) calculations have been used to show that macrophomate synthase... 

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