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The landmark DLVO theory of colloid stability sought to explain the stability of lyophobic colloids in terms of the interplay between attractive dispersion forces, and repulsive electrical (Coulombic) forces between particle surfaces. The net interaction energy between two particles (resulting from these so-called surface forces) as a function of surface separation can exhibit a maximum, a deep (primary) minimum and/or a shallow (secondary) minimum, giving stable, unstable or weakly flocculated dispersions. Other surface forces include steric forces arising from grafted or adsorbed polymer chains on the surfaces. Unadsorbed polymer can result in attractive depletion forces between particles, and polymer molecules that bridge particles can cause flocculation. Other forces mentioned are oscillatory structural forces, attractive hydrophobic forces and repulsive hydration forces between surfaces in water. Direct measurement of surface forces between both solid/liquid interfaces and between liquid/liquid interfaces is discussed at the end of the chapter.

In the late seventies and early eighties, a small number of researchers who had the requisite resources at their disposal made the first systematic attempts to employ the newly emerging quantum-chemical computational tools in experimental studies of molecular structures (for reviews see Boggs 1983G, 1988G; Schäfer et al. 1983G, 1987G, 1988aG; and Geise et al. 1988G). In this process, which provided an important testing ground for the evolution of computational chemistry, the ab initio geometric optimizations of glycine (Sellers et al. 1978AA) represent a special landmark. In a sequence of events unprecedented in conformational chemistry, the results of the optimizations first suggested the existence of a hidden conformation that had remained undetected in two independent microwave spectroscopic studies of the compound (Brown et al. 1978G; Suenram et al. 1978G), and then guided new experiments that led to the detection of the missing state (Suenram et al. 1980G; Schafer et al. 1980AA). In the first microwave investigations of glycine (Brown et al. 1978G; Guenram et al. 1978G)—experiments whose success represent a considerable achievement because glycine is difficult to work with in the vapor phase—the observed transitions were assigned to the cyclic form, C, of the compound. In both studies, it was emphasized that other conformers of glycine could have been present but were not detected in the microwave spectra because their line intensities were weaker than those of C. Nevertheless, since C was observed but not the stretched form, S, Brown et al. concluded that “the most likely conformation of glycine in the vapor state” is C and that the experimental result was in conflict with ab initio calculations of glycine by Vishveshwara and Pople (1977AA) in which S was found more stable than C. Brown et al. (1978G): “The microwave spectrum of glycine vapor has been measured and analyzed; it is in the molecular form with a dipole moment of 4.5–4.6D and probably having conformation (C), which is in conflict with a recent theoretical study that implies that conformation (S) is more stable.” In the sixties and seventies, theoretical chemistry had developed a somewhat uncertain reputation.

The change in the Gibbs free energy function, ΔG, of chemical reaction is determined by the difference between the heats respectively released to and absorbed from the environment, and separation of the enthalpy and entropy changes that these changes represent cannot be achieved without specific hypotheses as to their relations. The determination of the enthalpy of reaction by the plot of ΔG/T against 1/T (van’t Hoff plot) implicitly assumes that the enthalpy ΔH and entropy ΔS are temperature independent, and this assumption leads to very large errors when this is not the case and ΔH « TΔS. It is therefore inapplicable to the reactions of molecules, such as proteins, that have thermally activated local motions. The concepts offered previously by the author to relate the entropy and enthalpy changes in protein associations are reviewed briefly and applied to account for the temperature dependence of ΔH and ΔS. It is shown that two different values of the enthalpy computed in that manner correspond to each value of the apparent van’t Hoff enthalpy, but that the choice between the two is easily made by reference to the volume change on reaction. The enthalpies of association of subunit pairs of seven oligomers are all found to be positive and much more uniformly related to the size of the intersubunit surface than those previously assigned by use of the classical van’t Hoff plot.

Realistic molecular dynamics and self-assembly is represented in a lattice simulation where water, water-hydrocarbons, and water-amphiphilic systems are investigated. The details of the phase separation dynamics and the constructive self-assembly dynamics are discussed and compared to the corresponding experimental systems. The method used to represent the different molecular types can easily be expended to include additional molecules and thus allow the assembly of more complex structures. This molecular dynamics (MD) lattice gas fills a modeling gap between traditional MD and lattice gas methods. Both molecular objects and force fields are represented by propagating information particles and all microscopic interactions are reversible. Living systems, perhaps the ultimate constructive dynamical systems, is the motivation for this work and our focus is a study of the dynamics of molecular self-assembly and self-organization. In living systems, matter is organized such that it spontaneously constructs intricate functionalities at all levels from the molecules up to the organism and beyond. At the lower levels of description, chemical reactions, molecular selfassembly and self-organization are the drivers of this complexity. We shall, in this chapter, demonstrate how molecular self-assembly and selforganization processes can be represented in formal systems. The formal systems are to be denned as a special kind of lattice gas and they are in a form where an obvious correspondence exists between the observables in the lattice gases and the experimentally observed properties in the molecular self-assembly systems. This has the clear advantage that by using these formal systems, theory, simulation, and experiment can be conducted in concert and can mutually support each other. However, a disadvantage also exists because analytical results are difficult to obtain for these formal systems due to their inherent complexity dictated by their necessary realism. The key to novelt simpler molecules (from lower levels), dynamical hierarchies are formed [2, 3]. Dynamical hierarchies are characterized by distinct observable functionalities at multiple levels of description. Since these higher-order structures are generated spontaneously due to the physico-chemical properties of their building blocks, complexity can come for free in molecular self-assembly systems. Through such processes, matter apparently can program itself into structures that constitute living systems [11, 27, 30].