Fuzzy body

A molecule contains a nuclear distribution and an electronic distribution there is nothing else in a molecule. The nuclear arrangement is fully reflected in the electronic density distribution, consequently, the electronic density and its changes are sufficient to derive all information on all molecular properties. Molecular bodies are the fuzzy bodies of electronic charge density distributions consequently, the shape and shape changes of these fuzzy bodies potentially describe all molecular properties. Modern computational methods of quantum chemistry provide practical means to describe molecular electron distributions, and sufficiently accurate quantum chemical representations of the fuzzy molecular bodies are of importance for many reasons. A detailed analysis and understanding of "static" molecular properties such as "equilibrium" structure, and the more important dynamic properties such as vibrations, conformational changes and chemical reactions are hardly possible without a description of the molecule itself that implies a description of molecular bodies. 

This electron density p(r) corresponds to the fuzzy "body" of the electronic charge cloud, providing a representation for the shape of the molecule. 

In the general scheme described in subsequent sections, a functional group is regarded as a fuzzy body of electronic charge cloud, a fuzzy subset of the electronic charge density cloud of the complete molecule. In this context, a functional group is a special case of a fuzzy fragment of a molecular body, obtained by some subdivision... 

An example of the MEDLA electron density of bovine insulin protein is shown in Fig. 1, where the fuzzy body of the electronic density cloud is... 

FIGURE 1 The fuzzy body of the electron density of a bovine insulin molecule is represented by three molecular isodensity contour surfaces (MlDCOs), for the density thresholds of 0.1, 0.01, and 0.001 a.u. (atomic unit), respectively, as computed using the MEDLA method. Bovine insulin was among the proteins selected for the first ab initio quality electron density computations for macromolecules. ... 

Figure I.l A ball and stick model of the allyl alcohol molecule is shown. The formal bonding pattern is well recognizable in such "skeletal" models, however, the actual three-dimensional shape of the fuzzy "body" of the molecular electron density, ultimately responsible for chemical bonding, is not well represented.

Figure 1.2 The three-dimensional, fuzzy "body" of the charge density distribution of allyl alcohol can be represented by a series of "nested" molecular isodensity contours (MIDCO s). Along each MIDCO the electronic density is a constant value. Three such MIDCO s are shown for the constant electron density values of 0.2, 0.1, and 0.01 (in atomic units), respectively. A contour surface of lower density encloses surfaces of higher density. These MIDCO s are analogous to a series of Russian wooden dolls, each larger doll enclosing a smaller one. These ab initio MIDCO s have been calculated for the minimum energy conformation of allyl alcohol using a 6-31C basis set.

The three-dimensional shape of this fuzzy body of the electronic distribution has many important features not revealed by the simple, skeletal ball and stick model. One of the most important tasks of topological shape analysis of molecules is the precise analysis and concise description of the three-dimensional electronic charge distributions, such as that illustrated by the selected MIDCO s of allyl alcohol in Figure 1.2. Various methods and computational techniques of such topological shape analyses are discussed in detail in this book. 

This function p(r) represents the fuzzy body of the electronic charge cloud that in turn represents the shape of the molecule A. 

The ab initio molecular electronic density p(r),representing the fuzzy, electronic charge cloud, provides a detailed representation of the shape of the actual, fuzzy body of the molecule. 

This approach, however, can be generalized for any threshold value a, and one may consider the fuzzy molecular body as being viewed at various density thresholds, for the whole range of possible densities. An infinite family of formal bodies is obtained, and all these formal bodies, collectively, represent the actual molecular body. For each threshold value a, the formal, threshold-dependent molecular body is the density domain DD(a,K), defined as the collection of all those points r of the 3D space where the electronic density is greater than or equal to the threshold a,... 

The formal "bodies" of molecules do not have boundaries and the actual shape of molecules is determined by the fuzzy electron distribution. Realistic models describing molecular shapes and chemical bonding must reflect this natural fuzziness [27]. 

A fuzzy set B is called an R-deficient set if B has none of the point symmetry elements of family R. However, by analogy with the case of crisp sets, it takes only infinitesimal distortions to lose a given symmetry element. Consequently, unless further restrictions are applied, the total mass difference between a fuzzy set of a specified symmetry and another fuzzy set that does not have this symmetry can be infinitesimal. As a result, i -deficient fuzzy sets and fuzzy R sets can be almost identical. Nevertheless, the actual symmetry deficiencies of fuzzy continua, such as formal molecular bodies represented by fuzzy clouds of electron densities, can be defined in terms of the deviations from their maximal R subsets and minimal R supersets, defined in subsequent text. 

However, real molecules are quantum mechanical objects and they do not have a finite body defined in precise geometrical terms and a finite boundary surface that contains all the electron density of the molecule. The peripheral regions of a molecule can be better represented by a continuous, 3D electronic charge density function that approaches zero value at large distances from the nuclei of the molecule. This density function changes rapidly with distance within a certain range, but the change is continuous. The fuzzy, cloud-like electronic distribution of a molecule is very different from a macroscopic body [251], and no precise, finite distance can be specified that could indicate where the molecule ends. No true molecular surface exists in the classical, macroscopic sense. 

The characterization of the interrelations between chemical bonding and molecular shape requires a detailed analysis of the electronic density of molecules. Chemical bonding is a quantum mechanical phenomenon, and the shorthand notations of formal single, double, triple, and aromatic bonds used by chemists are a useful but rather severe oversimplification of reality. Similarly, the classical concepts of body and surface , the usual tools for the shape characterization of macroscopic objects, can be applied to molecules only indirectly. The quantum mechanical uncertainty of both electronic and nuclear positions within a molecule implies that valid descriptions of both chemical bonding and molecular shape must be based on the fuzzy, delocalize properties of electronic density distributions. These electron distributions are dominated by the nuclear arrangements and hence quantum mechanical uncertainly affects electrons on two levels by the lesser positional uncertainty of the more massive nuclei, and by the more prominent positional uncertainty of the electrons themselves. These two factors play important roles in chemistry and affect both chemical bonding and molecular shape. 

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