Partition/partitioning free energy

Let us consider one homologous series—generally indicated as /-series—and characterized by a given structural increment, for example, a CH2 group. At the same time, let us separate this series through a ID system where the separation coordinate is labeled as x. The partition free energy of the 11, component of the /-series is... 

The above relationship can be related to the change of partition free energies of members of homologous series due to the addition of a given structural increment or to any physical-chemical property that affects the retention. 

Figure 11.11 Thermodynamic relationship between partitioning free energies and free energies of solvation. Knowledge of any two free energies permits prediction of the third since any cycle around the free-energy triangle must sum to zero...

Each ion M+ N+ X and Y will generally have different energies in water and in an organic phase an ester such as dioctyladipate (low dielectric constant). The partition free energy... 

In the lattice model, the driving force for partitioning depends on the lattice coordination number z, which serves as a measure of the surface area of contact between the solute molecule and surrounding medium. It follows that Pj (A) -p j (B) should be a linear function of the sizes of solutes that partition between different media. Figure 16.10 shows examples in which the partitioning free energy increases linearly with the solute size. For the same reason, the Henry s law constant should increase with solute size. Figure 16.12 shows this result. 

The cleaning process proceeds by one of three primary mechanisms solubilization, emulsification, and roll-up [229]. In solubilization the oily phase partitions into surfactant micelles that desorb from the solid surface and diffuse into the bulk. As mentioned above, there is a body of theoretical work on solubilization [146, 147] and numerous experimental studies by a variety of spectroscopic techniques [143-145,230]. Emulsification involves the formation and removal of an emulsion at the oil-water interface the removal step may involve hydrodynamic as well as surface chemical forces. Emulsion formation is covered in Chapter XIV. In roll-up the surfactant reduces the contact angle of the liquid soil or the surface free energy of a solid particle aiding its detachment and subsequent removal by hydrodynamic forces. Adam and Stevenson s beautiful photographs illustrate roll-up of lanoline on wood fibers [231]. In order to achieve roll-up, one requires the surface free energies for soil detachment illustrated in Fig. XIII-14 to obey... 

Figure A2.2.1. Heat capacity of a two-state system as a function of the dimensionless temperature, lc T/([iH). From the partition fimction, one also finds the Helmholtz free energy as...

Since E = - 2 iU)tn., a given spin excess value 2m. implies a given energy partition. The free energy for such a specific energy partition is... 

It may be iisefiil to mention here one currently widely applied approximation for barrierless reactions, which is now frequently called microcanonical and canonical variational transition state theory (equivalent to the minimum density of states and maximum free energy transition state theory in figure A3,4,7. This type of theory can be understood by considering the partition fiinctions Q r ) as fiinctions of r similar to equation (A3,4.108) but with F (r ) instead of V Obviously 2(r J > Q so that the best possible choice for a... 

The canonical ensemble corresponds to a system of fixed and V, able to exchange energy with a thennal bath at temperature T, which represents the effects of the surroundings. The thennodynamic potential is the Helmholtz free energy, and it is related to the partition fiinction follows ... 

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 solubilization of diverse solutes in micelles is most often examined in tenns of partitioning equilibria, where an equilibrium constant K defines the ratio of the mole fraction of solute in the micelle (X and the mole fraction of solute in the aqueous pseudophase. This ratio serves to define the free energy of solubilization -RT In K). 

For these sequences the value of Gj, is less than a certain small value g. For such sequences the folding occurs directly from the ensemble of unfolded states to the NBA. The free energy surface is dominated by the NBA (or a funnel) and the volume associated with NBA is very large. The partition factor <6 is near unify so that these sequences reach the native state by two-state kinetics. The amplitudes in (C2.5.7) are nearly zero. There are no intennediates in the pathways from the denatured state to the native state. Fast folders reach the native state by a nucleation-collapse mechanism which means that once a certain number of contacts (folding nuclei) are fonned then the native state is reached very rapidly [25, 26]. The time scale for reaching the native state for fast folders (which are nonnally associated with those sequences for which topological fmstration is minimal) is found to be... 

Thus one must rely on macroscopic theories and empirical adjustments for the determination of potentials of mean force. Such empirical adjustments use free energy data as solubilities, partition coefficients, virial coefficients, phase diagrams, etc., while the frictional terms are derived from diffusion coefficients and macroscopic theories for hydrodynamic interactions. In this whole field of enquiry progress is slow and much work (and thought ) will be needed in the future. 

The HYBOT descriptors were successfully applied to the prediction of the partition coefficient log P (>i--octanol/water) for small organic componnds with one acceptor group from their calculated polarizabilities and the free energy acceptor factor C, as well as properties like solubility log S, the permeability of drugs (Caco-2, human skin), and for the modeling of biological activities. 

Two approaches to quantify/fQ, i.e., to establish a quantitative relationship between the structural features of a compoimd and its properties, are described in this section quantitative structure-property relationships (QSPR) and linear free energy relationships (LFER) cf. Section 3.4.2.2). The LFER approach is important for historical reasons because it contributed the first attempt to predict the property of a compound from an analysis of its structure. LFERs can be established only for congeneric series of compounds, i.e., sets of compounds that share the same skeleton and only have variations in the substituents attached to this skeleton. As examples of a QSPR approach, currently available methods for the prediction of the octanol/water partition coefficient, log P, and of aqueous solubility, log S, of organic compoimds are described in Section 10.1.4 and Section 10.15, respectively. 

The thermodynamic properties that we have considered so far, such as the internal energy, the pressure and the heat capacity are collectively known as the mechanical properties and can be routinely obtained from a Monte Carlo or molecular dynamics simulation. Other thermodynamic properties are difficult to determine accurately without resorting to special techniques. These are the so-called entropic or thermal properties the free energy, the chemical potential and the entropy itself. The difference between the mechanical emd thermal properties is that the mechanical properties are related to the derivative of the partition function whereas the thermal properties are directly related to the partition function itself. To illustrate the difference between these two classes of properties, let us consider the internal energy, U, and the Fielmholtz free energy, A. These are related to the partition function by ... 

LS now consider the problem of calculating the Helmholtz free energy of a molecular 1. Our aim is to express the free energy in the same functional form as the internal that is as an integral which incorporates the probability of a given state. First, we itute for the partition function in Equation (6.21) ... 

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. 

A consequence of writing the partition function as a product of a real gas and an ideal g part is that thermod)mamic properties can be written in terms of an ideal gas value and excess value. The ideal gas contributions can be determined analytically by integrating o the momenta. For example, the Helmholtz free energy is related to the canonical partitii function by ... 

Calculations of relative partition coefficients have been reported using the free energy perturbation method with the molecular dynamics and Monte Carlo simulation methods. For example, Essex, Reynolds and Richards calculated the difference in partition coefficients of methanol and ethanol partitioned between water and carbon tetrachloride with molecular dynamics sampling [Essex et al. 1989]. The results agreed remarkably well with experiment... 

The overall free energy can be partitioned into individual contributions if the thermo-lynamic integration method is used [Boresch et al. 1994 Boresch and Karplus 1995]. The itarting point is the thermodynamic integration formula for the free energy ... 

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