PHYSICAL FORCES AND MOLECULAR INTERACTIONS

While the Lifshitz model of atomic and molecular interactions performs nobly for the analysis of interactions of atoms, molecules, or particles in a continuous medium, when one reaches down to the atomic or molecular level, the concept of continuity must per force be abandoned atoms and molecules exist as definite individual species with defined (if fuzzily, at times) shapes and sizes. While we can understand, or at least rationalize, observed effects in the context defined by the Lifshitz and Hamaker models, once separation distances begin to approach molecular dimensions, we enter into a world in which the concept of continuity has no real physical meaning. Modern experimental techniques now allow us to reach to that level and the observed results demand new explanations. 

The ways Nature deals with chemicals are physical (force and heat) and/or chemical. Particularly important is the biological processes that are chanical prcxess at molecular level. Chemicals interact with the biological systems and are modified to the forms appropriate for them and, if toxic, may be rendered harmless in some cases. The biological and ecological systems, as a whole, know how to deal with those chemicals inherent in Nature, though individual organisms may or may not be able to cope with them all. 

The problems that occur when one tries to estimate affinity in terms of component terms do not arise when perturbation methods are used with simulations in order to compute potentials of mean force or free energies for molecular transformations simulations use a simple physical force field and thereby implicitly include all component terms discussed earlier. We have used the molecular transformation approach to compute binding affinities from these first principles [14]. The basic approach had been introduced in early work, in which we studied the affinity of xenon for myoglobin [11]. The procedure was to gradually decrease the interactions between xenon atom and protein, and compute the free energy change by standard perturbation methods, cf. (10). An (issential component is to impose a restraint on the... 

When a gas comes in contact with a solid surface, under suitable conditions of temperature and pressure, the concentration of the gas (the adsorbate) is always found to be greater near the surface (the adsorbent) than in the bulk of the gas phase. This process is known as adsorption. In all solids, the surface atoms are influenced by unbalanced attractive forces normal to the surface plane adsorption of gas molecules at the interface partially restores the balance of forces. Adsorption is spontaneous and is accompanied by a decrease in the free energy of the system. In the gas phase the adsorbate has three degrees of freedom in the adsorbed phase it has only two. This decrease in entropy means that the adsorption process is always exothermic. Adsorption may be either physical or chemical in nature. In the former, the process is dominated by molecular interaction forces, e.g., van der Waals and dispersion forces. The formation of the physically adsorbed layer is analogous to the condensation of a vapor into a liquid in fret, the heat of adsorption for this process is similar to that of liquefoction. 

Dispersion forces are ubiquitous and are present in all molecular interactions. They can occur in isolation, but are always present even when other types of interaction dominate. Typically, the interactions between hydrocarbons are exclusively dispersive and, because of them, hexane, at S.T.P., is a liquid boiling at 68.7°C and is not a gas. Dispersive interactions are sometimes referred to as hydrophobic or lyophobic particularly in the fields of biotechnology and biochemistry. These terms appear to have arisen because dispersive substances, e.g., the aliphatic hydrocarbons, do not dissolve readily in water. Biochemical terms for molecular interactions in relation to the physical chemical terms will be discussed later. 

A more practical approach for larger systems is molecular dynamics. In this method, the properties of bonds are determined through a combination of quantum-mechanical simulation and physical experiments, and stored in a database called a (semi-empirical) force field. Then a classical (non-quantum) simulation is done where bonds are modeled as spring-like interactions. Molecular... 

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