Organic molecules common features

This book deals with the organic chemistry of micelles, vesicles, micellar fibres, surface monolayers and a few 3D crystals formed by the assembly of synthetic surfactants in water or, less common, in organic solvents. Common features of these assemblies are molecular thinness and direct interaction of all their molecules with the environment, usually aqueous media. 

A common feature of die interaction of oxides with organic molecules is the breaking of C-H bonds, but rarely C-C bonds. The reaction to form CaHg... 

A common feature of the various methods that we have developed for the calculation of electronic effects in organic molecules is that they start from fundamental atomic data such as atomic ionization potentials and electron affinities, or atomic polarizability parameters. These atomic data are combined according to specific physical models, to calculate molecular descriptors which take account of the network of bonds. In other words, the constitution of a molecule (the topology) determines the way the procedures (algorithms) walk through the molecule. Again, as previously mentioned, the calculations are performed on the entire molecule. 

Such an ordered organization of biological photoreceptor molecules appears to be a common feature (which, of course, is hardly detected in more opaque, highly scattering biological material). In the vertebrate rod maximum absorption lies in membranes (discs) perpendicular to the long axis of the rods, but anisotropically within these planes47). 

We can see the different structural features of n-pentane, Ao-pentane, and neo-pentane more clearly by drawing the molecules in two dimensions, as shown in the middle row of Figure 12.1. Alternatively, we can represent them by the stick structures shown in the bottom row. A stick structure is a commonly used, shorthand notation for representing an organic molecule. Each line (stick)... 

Catalysis is an important field in both academic and industrial research because it leads to more efficient reactions in terms of energy consumption and waste production. The common feature of these processes is a catalytically active species which forms reactive intermediates by coordination of an organic ligand and thus decreases the activation energy. Formation of the product should occur with regeneration of the catalytically active species. The efficiency of the catalyst can be described by its turnover number, providing a measure of how many catalytic cycles are passed by one molecule of catalyst. 

This review discusses several approaches for the automatic identification of common structural features or structural similarity of organic molecules. The organization of the chapter is as follows. Section 2 gives an overview of the methods for structural feature analysis. Identification of common structural features is discussed in Sect. 3 with a few applications in structure-activity studies, which is subsequently followed by the identification of structural similarity in Sect. 4. The quantification of structural similarity is discussed in Sect. 5. The basic algorithms of these approaches and the relative software systems are also referred to with some illustrative examples. 

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