Topological molecular shape

THE TOPOLOGICAL MOLECULAR SHAPE AND SIMILARITY ANALYSIS THE SHAPE GROUP METHOD... 

One can describe a molecule in many ways and the same applies to bioisosteres. Molecular descriptor methods are covered in the third part by the application of different representations. A number of computational approaches to bioisosteric replacement are covered in chapters on physicochemical properties, molecular topology, molecular shape, and the use of protein structure information. Each chapter covers many common methods and overviews of when best to apply these methods, and where they have been successfully applied. 

IV. Three-dimensional topological molecular shape characterization... 

Up to this point, we have emphasized the stereochemical properties of molecules as objects, without concern for processes which affect the molecular shape. The term dynamic stereochemistry applies to die topology of processes which effect a structural change. The cases that are most important in organic chemistry are chemical reactions, conformational changes, and noncovalent complex formation. In order to understand the stereochemical aspects of a dynamic process, it is essential not only that the stereochemical relationship between starting and product states be established, but also that the spatial features of proposed intermediates and transition states must account for the observed stereochemical transformations. 

Mezey, P.G. (1993) Shape in Chemistry An Introduction to Molecular Shape and Topology, VCH Publishers, New York. 

Mezey, P.G. (1995) Methods of molecular shape-similarity analysis and topological shape design. 

Steric parameters include bond length, bond angle, bond torsion, conformation, topology or connection among atoms in the molecule, symmetry, moment of inertia, molecular diameter, molecular surface area, molecular volume, and molecular shape. 

The name lepidopterene refers to the hydrocarbon 113 (L) whose butterflylike molecular shape was first revealed by X-ray diffraction analysis [129,130]. The structured electronic absorption spectra of lepidopterenes around 270 nm closely resemble that of 9,10-dihydroanthracene (see Figure 31). However, in terms of excited state properties, lepidopterenes have very little in common with 9,10-dihydroanthracene, which in solution fluoresces with a quantum yield of 0.16. By contrast, photoexcitation of lepidopterenes leads mainly to intramolecular exciplexes of 7i-chromophorically substituted anthracenes in an adiabatic process, for which both the molecular topology... 

It should also be noted that the stability of the distinct mesophases can be quite different. It seems that there is a significant effect of molecular shape and topology, stabilizing SmA phases in the system 41/43 and Colhex phases in the system 35/37. In addition, the mesophase stability is often reduced close to the transition to another mesophase (see Fig. 15). Hence, the order-disorder temperatures can only be roughly estimated based on segmental solubility parameters [24, 25]. 

Biodegradation by metabolic processes Molecular connectivity index (topological indices - shape) Molar refractivity Field constants atomic charges... 

Mezey PG (1993) In Shape in Chemistry. An introduction to molecular shape and topology, VCH Publishers, New York... 

A chemical reaction can be viewed as a phenomenon dealing with molecular shape (topology) changes. Whether a particular reaction will take place will depend upon whether the product can fit within the space occupied by the reactant. The space occupied by the reactant is the reaction cavity. Since the boundaries of a reaction cavity are undefined in an isotropic solution, size matching of the reactant, products and the reaction cavity is not important in this medium. On the other hand, when the reaction cavity has a well-defined boundary, as in most organized assemblies (especially in solid state), size matching can become important and occasionally may even become the sole factor controlling the feasibility of a reaction (Fig. 8). 

Mezey, P.G.,"Methods of Molecular Shape-Similarity Analysis and Topological Shape Design". In Dean, P.M., ed., Molecular Similarity in Drug Design (Chapman Hall - Blackie Publishers, Glasgow, U.K., 1995). 

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