Structure-directing forces

Interactions between macromolecules (protems, lipids, DNA,.. . ) or biological structures (e.g. membranes) are considerably more complex than the interactions described m the two preceding paragraphs. The sum of all biological mteractions at the molecular level is the basis of the complex mechanisms of life. In addition to computer simulations, direct force measurements [98], especially the surface forces apparatus, represent an invaluable tool to help understand the molecular interactions in biological systems. 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

P. Kekicheff, P. Richetti, H. K. Christenson. Structure and elastic properties of lamellar mesophases from direct force measurements. Langmuir 7 1874-1879, 1991. 

Phthalocyanines have attracted particular attention as potential surface modifiers due to their stability and tendency to form ordered structures directed by dispersion forces. They are inherently host-guest structures with a readily interchangeable coordinating metal ion, which in the solid state results in a tunable bandgap. At a surface, in addition to possibly interesting electronic... 

There are several ways to model the substrate. The simplest would be to consider the substrate as a structureless attractive wall. However, since we want the polymer molecules to be parallel to each other on the substrate, we impose a directional force. In 2D crystallization, we took the substrate structure into account by use of the continuous substrate potential t/2, a sort of mean field potential that restricts the molecular motion on the substrate [20] ... 

Finally, an important if tentative conclusion emerges concerning the symmetry of distribution functions, which could be relevant to the general theory of polarization and to current ideas about liquid structure. Theoretical analysis in terms of radially symmetric models does not necessarily tell us about the structure of a system, because the short-range forces, by their very nature, have a directional character which is not lost in any averaging process. Is it this averaged directional force which is responsible for structure in liquids and solutions ... 

However, directionality of individual non-covalent interactions is not always needed and even non-directional forces such as the hydrophobic effect can be utilized for the preparation of interlocked structures. Cyclodextrins may serve as a first example. They are macrocycles built from a-glycosidic D-glucose subunits. While their hydrophilic, OH group-decorated surface makes them water soluble, they bear a lipophilic... 

Israelachvili, J. 1987. Solvation forces and liquid structure, as probed by direct force measurements. Acc. Chem. Res. 20 415-421. 

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