Similarity three-dimensional

Catherine Pepperrell, Three-Dimensional Similarity Searching, Research Studies Press, Taunton, UK, 1994. 

Electrons cannot move haphazardly. Their movement around an atomic nucleus is restricted to fixed regions of space. These regions are three-dimensional, similar to the layers of an onion. 

Integration of Three-dimensional Substructure Searching and Molecular Modeling Three-dimensional Similarity Searching... 

Renner, S., Schwab, C.H., Gasteiger, J., and Schneider, G. (2006) Impact of conformational flexibility on three-dimensional similarity searching using... 

The emerging techniques for computer recognition of the similarity of three-dimensional properties of molecules will be discussed in this review. In particular, we will concentrate on methods or computer programs that examine a database of three-dimensional structures. However, to place such programs in context we will introduce the concepts of chemical information and the terminology, usually derived from molecular graphics, of three-dimensional similarity. Since much of the impetus for this research has been from research on computer-assisted design of bioactive molecules, this field will be introduced also. 

The study of structure-reactivity relationships by the organic chemist Hammett showed that there is often a quantitative relationship between the two-dimensional structure of organic molecules and their chemical reactivity. Specifically, he correlated the changes in chemical properties of a molecule that result from a small change in its chemical structure that is, the quantitative linear relationship between electron density at a certain part of a molecule and its tendency to undergo reactions of various types at that site. For example, there is a linear relationship between the effea of remote substituents on the equilibrium constant for the ionization of an acid with the effect of these substituents on the rate or equilibrium constant for many other types of chemical reaction. The relative value of Hammett substituent constants describes the similarity of molecules in terms of electronic properties. Taft expanded the method to include the steric hindrance of access of reagents to the reaction site by nearby substituents, a quantitation of three-dimensional similarity. In addition, Charton, Verloop, Austel, and others extended and refined these ideas. Finally, Hansch and Fujita showed that biological activity frequently is also quantitatively correlated with the hydrophobic character of the substituents. They coined the term QSAR, Quantitative Structure-Activity Relationships, for this type of analysis. 

Precise definitions are needed if one is to use a program to recognize three-dimensional similarity. In this section we will discuss a variety of such definitions. Additionally, we will show how such definitions are used to recognize the proposed three-dimensional features that are common to a set of molecules, an especially important problem with structurally complex natural produas. 

Three-Dimensional Similarity Based on Geometric Properties... 

It can be seen that the definition of three-dimensional similarity is not a solved problem but rather an area of active research. It is possible that the most appropriate definition will depend on the structures of the molecules investigated and on the property to be compared. Thus, computer programs that perform three-dimensional searches might need to include a variety of definitions of similarity. 

Finally, the interaction of the mixture components can occur via the cluster-topotaxic mechanism when structures of the starting compound and the product of MA are similar. This mechanism includes the oriented interaction when all or part of the crystal structure of the initial component is retained in the target product. For a topotactic transformation, a three-dimensional similarity between the structures of a starting material and product is important but not obligatory, and even the compositions may differ radically [81-83], Such interaction of the components during the milling occurs without the formation of an amorphous state of the mixture and proceeds faster than interaction of the same components through the plastic deformation or dissociative mechanism [47],... 

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