Thermodynamics and interactions

Like all material things, the structure and behaviour of biological systems are governed by the interplay between thermal motion of molecules and the various interaction forces between them. This chapter reviews the basics of thermodynamic equilibrium at the molecular level, leading to ways in which we can measure the various components of thermodynamic forces in biomolecular systems. 

After working through this chapter you should be able to  

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The adsorption of mixed surfactants at the air—water interface (monolayer formation) is mechanistically very similar to mixed micelle formation. The mixed monolayer is oriented so that the surfactant hydrophilic groups are adjacent to each other. The hydrophobic groups are removed from the aqueous environment and are in contact with other hydrophobic groups or air. Therefore, the forces tending to cause monolayers to form are similar to those causing micelles to form and the thermodynamics and interactions between surfactants are similar in the two aggregation processes. 

One of the constant concerns of numerous industries where either aerosols or toxic vapors are produced is the effects of these upon workers. A variety of health problems arise because of the workers inhaling gases and aerosols of irritant or toxic fibers which are produced in the normal course of activities. A less obvious hazard arises from the attachment of trace molecular species to particles. If these trace species are radioactive or chemically toxic, the particles, which effectively concentrate them, provide a vehicle for delivery deep within the body causing a health hazard far beyond that suggested by their gross molecular concentration in the air [1.31,32]. Kinetic theory, thermodynamics, and interaction forces, all enter into descriptions of the attachment process. 

Atmospheric visibility can be greatly decreased by primary particulate emissions from industrial sources and by particles generated or grown in the atmosphere in addition to naturally occurring causes. Since the visibility reduction is a function of particle size distribution, aerosol thermodynamics and interaction forces are involved in addition to light scattering. 

A second way of dealing with the relationship between aj and the experimental concentration requires the use of a statistical model. We assume that the system consists of Nj molecules of type 1 and N2 molecules of type 2. In addition, it is assumed that the molecules, while distinguishable, are identical to one another in size and interaction energy. That is, we can replace a molecule of type 1 in the mixture by one of type 2 and both AV and AH are zero for the process. Now we consider the placement of these molecules in the Nj + N2 = N sites of a three-dimensional lattice. The total number of arrangements of the N molecules is given by N , but since interchanging any of the I s or 2 s makes no difference, we divide by the number of ways of doing the latter—Ni and N2 , respectively—to obtain the total number of different ways the system can come about. This is called the thermodynamic probabilty 2 of the system, and we saw in Sec. 3.3 that 2 is the basis for the statistical calculation of entropy. For this specific model... 

Although the chiral recognition mechanism of these cyclodexttin-based phases is not entirely understood, thermodynamic and column capacity studies indicate that the analytes may interact with the functionalized cyclodextrins by either associating with the outside or mouth of the cyclodextrin, or by forming a more traditional inclusion complex with the cyclodextrin (122). As in the case of the metal-complex chiral stationary phase, configuration assignment is generally not possible in the absence of pure chiral standards. 

The kinetic theory attempts to describe the individual molecules energies and interactions statistical thermodynamics attempts to fundamentally develop the equation of state from considerations of groupings of molecules. These approaches are complementary in many ways (3,123,124). A weU-referenced text covering molecular thermodynamics is also available (125). 

The theory of quenched-annealed fluids is a rapidly developing area. In this chapter we have attempted to present some of the issues already solved and to discuss only some of the problems that need further study. Undoubtedly there remains much room for theoretical developments. On the other hand, accumulation of the theoretical and simulation results is required for further progress. Of particular importance are the data for thermodynamics and phase transitions in partly quenched, even quite simple systems. The studies of the models with more sophisticated interactions and model complex fluids, closer to the systems of experimental focus and of practical interest, are of much interest and seem likely to be developed in future. 

The non-bonded interaction energy, the van-der-Waals and electrostatic part of the interaction Hamiltonian are best determined by parametrizing a molecular liquid that contains the same chemical groups as the polymers against the experimentally measured thermodynamical and dynamical data, e.g., enthalpy of vaporization, diffusion coefficient, or viscosity. The parameters can then be transferred to polymers, as was done in our case, for instance in polystyrene (from benzene) [19] or poly (vinyl alcohol) (from ethanol) [20,21]. 

In this section the interaction of a metal with its aqueous environment will be considered from the viewpoint Of thermodynamics and electrode kinetics, and in order to simplify the discussion it will be assumed that the metal is a homogeneous continuum, and no account will be taken of submicroscopic, microscopic and macroscopic heterogeneities, which are dealt with elsewhere see Sections 1.3 and 20.4). Furthermore, emphasis will be placed on uniform corrosion since localised attack is considered in Section 1.6. 

Lamb, J. D., Izatt, R. M., Christensen, J. J., Eatough, D. J. Thermodynamics and Kinetics of Cation-Macrocycle Interaction, in Coordination Chemistry of Macrocyclic Compounds (ed. Melson, G. A.), p. 145-217, New York, Plenum Press 1979... 

The kinetics of decomposition of these solids may be classified according to the process which has been identified as rate-limiting. This criterion allows a more concise presentation but is not completely satisfactory since some reactions show a sensitivity of behaviour to the conditions prevailing [1270]. Furthermore, certain of the reactions discussed are reversible. Reference to the extensive literature devoted to the thermodynamic properties of these solids and phase stabilities and interactions will only be made where kinetic observations or arguments have been used. 

In view of the above developments, it is now possible to formulate theories of the complex phase behavior and critical phenomena that one observes in stractured continua. Furthermore, there is currently little data on the transport properties, rheological characteristics, and thermomechaiucal properties of such materials, but the thermodynamics and dynamics of these materials subject to long-range interparticle interactions (e.g., disjoiiung pressure effects, phase separation, and viscoelastic behavior) can now be approached systematically. Such studies will lead to sigiuficant intellectual and practical advances. 

A more sophisticated understanding is linked to an appreciation of the interaction of thermodynamic and kinetic considerations and is likely to be dependent upon the ability to visualise some form of mental model involving molecular collisions and interactions (Gilbert, 2005). This allows the student to see that two reactions are occurring simultaneously ... 

Interactions between thermodynamics and kinetics are sometimes given short shrift. The following article will help remedy this omission ... 

Ogston, AG SUpananta, P, The Thermodynamics of Interaction between Sephadex and Penetrating Solntes, Biochemical Jonmal 116, 171, 1970. 

Later we shall see how fundamental quantities such as /i can be estimated from first principles (via a basic knowledge of the molecule such as its molecular weight, rotational constants etc.) and how the equilibrium constant is derived by requiring the chemical potentials of the interacting species to add up to zero as in Eq. (20). The above equations relate kinetics to thermodynamics and enable one to predict the rate constant for a reaction in the forward direction if the rate constant for the reverse reaction as well as thermodynamic data is known. 

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