Statistical mechanics free energy

The reason we prefer to use 1 M for the standard state in both the gas phase and in liquid solution is that using the same concentration in the gas phase and solution eliminates an entropic term in the statistical mechanical free energy and allows us to focus on the interaction terms coupling the solute to the solvent. In particular, using the standard state of Equation 67, we can write the free energy of solvation of a rigid, non-rotating solute as... 

DeBolt, S.E. and Kollman, P.A. (1990) A Theoretical Examination of Solva-tochromism and Solute-Solvent Structuring in Simple Alkyl Carbonyl Compounds. Simulations Using Statistical Mechanical Free Energy Perturbation Methods, J. Am. Chem. Soc. 112, 7515-7524. 

The partitionfunction of the system contains a Boltzmann lattice-energy factor, a combinatorial factor representing the entropy of segment mixing and empty lattice sites, and a statistical-mechanical free-volume term. From the partition function, the equation of state may be calculated in the form of... 

A quantitative theory of rate processes has been developed on the assumption that the activated state has a characteristic enthalpy, entropy and free energy the concentration of activated molecules may thus be calculated using statistical mechanical methods. Whilst the theory gives a very plausible treatment of very many rate processes, it suffers from the difficulty of calculating the thermodynamic properties of the transition state. 

If one denotes the averages over a canonical distribution by (.. . ), then the relation A = U-T S and U = (W) leads to the statistical mechanical coimection to the themiodynamic free energy A ... 

Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F. Statistical mechanics and molecular dynamics The calculation of free energy, in Molecular Dynamics and Protein Structure, J. Hermans, ed.. Polycrystal Book Service, PO Box 27, Western Springs, 111., USA, (1985) 43-46. 

To reiterate a point that we made earlier, these problems of accurately calculating the free energy and entropy do not arise for isolated molecules that have a small number of well-characterised minima which can all be enumerated. The partition function for such systems can be obtained by standard statistical mechanical methods involving a summation over the mini mum energy states, taking care to include contributions from internal vibrational motion. 

The concept of corresponding states was based on kinetic molecular theory, which describes molecules as discrete, rapidly moving particles that together constitute a fluid or soHd. Therefore, the theory of corresponding states was a macroscopic concept based on empirical observations. In 1939, the theory of corresponding states was derived from an inverse sixth power molecular potential model (74). Four basic assumptions were made (/) classical statistical mechanics apply, (2) the molecules must be spherical either by actual shape or by virtue of rapid and free rotation, (3) the intramolecular vibrations are considered identical for molecules in either the gas or Hquid phases, and (4) the potential energy of a coUection of molecules is a function of only the various intermolecular distances. 

A statistical mechanical fonnulation of implicit solvent representations provides a robust theoretical framework for understanding the influence of solvation biomolecular systems. A decomposition of the free energy in tenns of nonpolar and electrostatic contributions, AVF = AVF " + AVF ° , is central to many approximate treatments. An attractive and widely used treatment consists in representing the nonpolar contribution AVF " by a SASA surface tension term with Eq. (15) and the electrostatic contribution by using the... 

It is possible to go beyond the SASA/PB approximation and develop better approximations to current implicit solvent representations with sophisticated statistical mechanical models based on distribution functions or integral equations (see Section V.A). An alternative intermediate approach consists in including a small number of explicit solvent molecules near the solute while the influence of the remain bulk solvent molecules is taken into account implicitly (see Section V.B). On the other hand, in some cases it is necessary to use a treatment that is markedly simpler than SASA/PB to carry out extensive conformational searches. In such situations, it possible to use empirical models that describe the entire solvation free energy on the basis of the SASA (see Section V.C). An even simpler class of approximations consists in using infonnation-based potentials constructed to mimic and reproduce the statistical trends observed in macromolecular structures (see Section V.D). Although the microscopic basis of these approximations is not yet formally linked to a statistical mechanical formulation of implicit solvent, full SASA models and empirical information-based potentials may be very effective for particular problems. 

In the present case, each endpoint involves—in addition to the fully interacting solute—an intact side chain fragment without any interactions with its environment. This fragment is equivalent to a molecule in the gas phase (acetamide or acetate) and contributes an additional term to the overall free energy that is easily calculated from ideal gas statistical mechanics [18]. This contribution is similar but not identical at the two endpoints. However, the corresponding contributions are the same for the transfonnation in solution and in complex with the protein therefore, they cancel exactly when the upper and lower legs of the thermodynamic cycle are subtracted (Fig. 3a). 

In the previous section we saw on an example the main steps of a standard statistical mechanical description of an interface. First, we introduce a Hamiltonian describing the interaction between particles. In principle this Hamiltonian is known from the model introduced at a microscopic level. Then we calculate the free energy and the interfacial structure via some approximations. In principle, this approach requires us to explore the overall phase space which is a manifold of dimension 6N equal to the number of degrees of freedom for the total number of particles, N, in the system. 

The Gibbs free energy is given in terms of the enthalpy and entropy, G — H — TS. The enthalpy and entropy for a macroscopic ensemble of particles may be calculated from properties of the individual molecules by means of statistical mechanics. 

In the PPF, the first factor Pi describes the statistical average of non-correlated spin fiip events over entire lattice points, and the second factor P2 is the conventional thermal activation factor. Hence, the product of P and P2 corresponds to the Boltzmann factor in the free energy and gives the probability that on<= of the paths specified by a set of path variables occurs. The third factor P3 characterizes the PPM. One may see the similarity with the configurational entropy term of the CVM (see eq.(5)), which gives the multiplicity, i.e. the number of equivalent states. In a similar sense, P can be viewed as the number of equivalent paths, i.e. the degrees of freedom of the microscopic evolution from one state to another. As was pointed out in the Introduction section, mathematical representation of P3 depends on the mechanism of elementary kinetics. It is noted that eqs.(8)-(10) are valid only for a spin kinetics. 

Treatment of Solutions by Statistical Mechanics. Since the vapor pressure is directly connected with the free energy, in the thermodynamic treatment the free energy is discussed first, and the entropy is derived from it. In the treatment by statistical mechanics, however, the entropy is discussed first, and the free energy is derived from it. Let us first consider an element that consists of a single isotope. When the particles share a certain total energy E, we are interested in the number of recog-... 

The manner in which a film is formed on a surface by CVD is still a matter of controversy and several theories have been advanced to describe the phenomena. ] A thermodynamic theory proposes that a solid nucleus is formed from supersaturated vapor as a result of the difference between the surface free energy and the bulk free energy of the nucleus. Another and newer theory is based on atomistic nucle-ation and combines chemical bonding of solid surfaces and statistical mechanics. These theories are certainly valuable in themselves but considered outside the scope of this book. 

Another simple approach assumes temperature-dependent AH and AS and a nonlinear dependence of log k on T (123, 124, 130). When this dependence is assumed in a particular form, a linear relation between AH and AS can arise for a given temperature interval. This condition is met, for example, when ACp = aT" (124, 213). Further theoretical derivatives of general validity have also been attempted besides the early work (20, 29-32), particularly the treatment of Riietschi (96) in the framework of statistical mechanics and of Thorn (125) in thermodynamics are to be mentioned. All of the too general derivations in their utmost consequences predict isokinetic behavior for any reaction series, and this prediction is clearly at variance with the facts. Only Riietschi s theory makes allowance for nonisokinetic behavior (96), and Thorn first attempted to define the reaction series in terms of monotonicity of AS and AH (125, 209). It follows further from pure thermodynamics that a qualitative compensation effect (not exactly a linear dependence) is to be expected either for constant volume or for constant pressure parameters in all cases, when the free energy changes only slightly (214). The reaction series would thus be defined by small differences in reactivity. However, any more definite prediction, whether the isokinetic relationship will hold or not, seems not to be feasible at present. 

The necessity of the statistical approach has to be stressed once more. Any statement in this topic has a definitely statistical character and is valid only with a certain probability and in certain range of validity, limited as to the structural conditions and as to the temperature region. In fact, all chemical conceptions can break dovra when the temperature is changed too much. The isokinetic relationship, when significantly proved, can help in defining the term reaction series it can be considered a necessary but not sufficient condition of a common reaction mechanism and in any case is a necessary presumption for any linear free energy relationship. Hence, it does not at all detract from kinetic measurements at different temperatures on the contrary, it gives them still more importance. 

The importance of solvation on reaction surfaces is evident in striking medium dependence of reaction rates, particularly for polar reactions, and in variations of product distributions as for methyl formate discussed above and of relative reactivities (18,26). Thus, in order to obtain a molecular level understanding of the influence of solvation on the energetics and courses of reactions, we have carried out statistical mechanics simulations that have yielded free energy of activation profiles (30) for several organic reactions in solution (11.18.19.31. ... 

Various statistical treatments of reaction kinetics provide a physical picture for the underlying molecular basis for Arrhenius temperature dependence. One of the most common approaches is Eyring transition state theory, which postulates a thermal equilibrium between reactants and the transition state. Applying statistical mechanical methods to this equilibrium and to the inherent rate of activated molecules transiting the barrier leads to the Eyring equation (Eq. 10.3), where k is the Boltzmann constant, h is the Planck s constant, and AG is the relative free energy of the transition state [note Eq. (10.3) ignores a transmission factor, which is normally 1, in the preexponential term]. 

---