Free energy directed approach

Gibbs ensemble. Good for obtaining a few points for subcritical phase coexistence between phases of moderate densities does not provide free energies directly. Primarily used to study fluid (disordered) phases. Is a standalone approach, and requires modest programming and computational effort to set up and equilibrate the multiple simulation boxes. Provides accurate coexistence points at intermediate temperatures below the critical point but with sufficient thermal mobility to equilibrate. 

Some people prefer to use the multiple time step approach to handle fast degrees of freedom, while others prefer to use constraints, and there are situations in which both techniques are applicable. Constraints also find an application in the study of rare events, where a system may be studied at the top of a free energy barrier (see later), or for convenience when it is desired to fix a thennodynamic order parameter or ordering direction... 

A major drawback of MD and MC techniques is that they calculate average properties. The free energy and entropy fiinctions caimot be expressed as simple averages of fimctions of the state point y. They are directly coimected to the logaritlun of the partition fiinction, and our methods do not give us the partition fiinction itself Nonetheless, calculating free energies is important, especially when we wish to detennine the relative thenuodynamic stability of different phases. How can we approach this problem ... 

The alternative to direct simulation of two-phase coexistence is the calculation of free energies or chemical potentials together with solution of the themiodynamic coexistence conditions. Thus, we must solve (say) pj (P) = PjjCT ) at constant T. A reasonable approach [173. 174. 175 and 176] is to conduct constant-AT J simulations, measure p by test-particle insertion, and also to note that the simulations give the derivative 3p/3 7 =(F)/A directly. Thus, conducting... 

Brown developed the selectivity relationship before the introduction of aromatic reactivities following the Hammett model. The former, less direct approach to linear free-energy relationships was necessary because of lack of data at the time. 

More detailed aspects of protein function can be obtained also by force-field based approaches. Whereas protein function requires protein dynamics, no experimental technique can observe it directly on an atomic scale, and motions have to be simulated by molecular dynamics (MD) simulations. Also free energy differences (e.g. between binding energies of different protein ligands) can be characterised by MD simulations. Molecular mechanics or molecular dynamics based approaches are also necessary for homology modelling and for structure refinement in X-ray crystallography and NMR structure determination. 

Many researchers have applied similar approaches to develop or apply linear free energy relationships, when the substituent is directly attached to the double bond, with some success. Two of the more notable examples can be found in the Patterns of Reactivity Scheme (Section 7.3.4) and the works of Giese and coworkers.16 19... 

The free energies of activation for the one reaction series are directly proportional to the standard free energy changes for another. This form is emphasized by Eq. (10-3), and is what gives rise to the designation of this approach as an LFER. 

The application of the overpotential t] can be considered to be equivalent to the displacement of the potential energy curves by the amount 7]F with respect to each other. The high field is now applied across the double layer between the electrode and the ions at the plane of closest approach. It is apparent from Fig. 12 that the energy of activation in the favoured direction will be diminished by etrjF while that in the reverse direction will be increased by (1 — ac)r]F where the simplest interpretation of a is in terms of the slopes of the potential energy curves (a = mi/ mi+m )) at the points of intersection electrode processes indeed are the classical example of linear free energy relations. 

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]. 

The quality of the mean-field approximation can be tested in simulations of the same lattice model [13]. Ideally, direct free-energy calculations of the liquid and solid phases would allow us to locate the point where the two phases coexist. However, in the present studies we followed a less accurate, but simpler approach we observed the onset of freezing in a simulation where the system was slowly cooled. To diminish the effect of supercooling at the freezing point, we introduced a terraced substrate into the system to act as a crystallization seed [14]. We verified that this seed had little effect on the phase coexistence temperature. For details, see Sect. A.3. At freezing, we have... 

In the remainder of this chapter, we review the fundamentals that underlie the theoretical developments in this book. We outline, in sequence, the concept of density of states and partition function, the most basic approaches to calculating free energies and the essential strategies for improving the efficiency of these calculations. The ideas discussed here are, most likely, known to the reader. They can also be found in classical books on statistical mechanics [132-134] and molecular simulations [135, 136]. Thus, we do not attempt to be exhaustive. On the contrary, we present the material in a way that is most directly relevant to the topics covered in the book. 

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