Molecular three dimensional specificity

QSAR theories are convenient for the design of new analogs of a known active compound but these theories are not always able to go beyond the chemical frame of the particular family studied. Considering structure-activity studies in the light of the three dimensional specificity of molecular interactions between drugs and receptors, conformational properties appear to be essential. 

SMILES (simplified molecular-input line-entry specification) a way of specifying a molecular formula and connectivity, but not the three-dimensional geometry... 

SAMs provide the needed design flexibUity, both at the individual molecular and at the material levels, and offer a vehicle for investigation of specific interactions at interfaces, and of the effect of increasing molecular complexity on the stmcture and stabUity of two-dimensional assembHes. These studies may eventuaUy produce the design capabUities needed for assembHes of three-dimensional stmctures (109). 

Enzymes are excellent catalysts for two reasons great specificity and high turnover rates. With but few exceptions, all reac tions in biological systems are catalyzed by enzymes, and each enzyme usually catalyzes only one reaction. For most of the important enzymes and other proteins, the amino-acid sequences and three-dimensional structures have been determined. When the molecular struc ture of an enzyme is known, a precise molecular weight could be used to state concentration in molar units. However, the amount is usually expressed in terms of catalytic activity because some of the enzyme may be denatured or otherwise inactive. An international unit (lU) of an enzyme is defined as the amount capable of producing one micromole of its reaction product in one minute under its optimal (or some defined) reaction conditions. Specific activity, the activity per unit mass, is an index of enzyme purity. 

The present review intends to be illustrative rather than comprehensive, and focuses on the results of this study leading to the hypothesis 9 — the three-dimensional shape similarity between interacting groups in reacting molecules is responsible for more specific and precise molecular recognition than would otherwise be achieved — and on the explanation of biological recognition on this basis. 

The similarity recognition hypothesis presented here would be applicable to the specific and precise discrimination in chemical and biological systems. It is hoped that this review will serve to stimulate further work on the physicochemical origin of the shape-similarity effect on specific molecular recognition, for example, work on weak interactions specific for the three-dimensional shape of interacting groups. 

To picture the spatial distribution of an electron around a nucleus, we must try to visualize a three-dimensional wave. Scientists have coined a name for these three-dimensional waves that characterize electrons they are called orbitals. The word comes from orbit, which describes the path that a planet follows when it moves about the sun. An orbit, however, consists of a specific path, typically a circle or an ellipse. In contrast, an orbital is a three-dimensional volume for example, a sphere or an hourglass. The shape of a particular orbital shows how an atomic or a molecular electron fills three-dimensional space. Just as energy is quantized, orbitals have specific shapes and orientations. We describe the details of orbitals in Section 7-1. 

Enzymes are proteins, i.e. sequences of amino acids linked by peptide bonds. The sequence of amino acids within the polypeptide chain is characteristic of each enzyme. This leads to a specific three-dimensional conformation for each enzyme in which the molecular chains are folded in such a way that certain key amino acids are situated in specific strategic locations. This folded arrangement, together with the positioning of key amino acids, gives rise to the remarkable catalytic activity associated with enzymes. 

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