Conformational analysis. See

Structure A typical alicyclic hydrocarbon. It exists in two modifications called the boat and the chair, as shown. This is due to slight distortion of the bond angles in accordance with the modified version of Baeyer s strain theory. Cyclohexane has been studied extensively on a theoretical basis in a branch of advanced chemistry called conformational analysis. See conformation. 

Cluster analysis was considered in our discussion of conformational analysis (see Section 9.13) for compound selection one would typically want to select a representative molecule or molecules from each cluster. A practical consideration when deciding which cluster analysis method to use is that for large numbers of molecules some algorithms may not be feasible because they require an excessive amount of memory or may have a long execution time. Another consideration with cluster analysis (and with some of the other methods that we will discuss) is the need to calculate the distance between each pair of molecules from the vector of descriptors (or from their scaled derivatives or from a set of principal components, if these are being used). For binary descriptors such as molecular fingerprints this distance is often given by 1 — S, where S is the similarity coefficient (Table 12.3). 

Saddle points, just like passes in a mountain area, provide the easiest way to pass from one valley to another. On the PES. saddle points therefore represent transition states providing the lowest energy barriers for conformational interconversions. The goal of conformational analysis (see Conformational Analysis 2 Conformational Analysis 3 and Conformational Anafysis Homotopy) is to find the set of interrelated energy minima and saddle points revealing the network of conformational interconversions (NCI). The NCI describes the dynamics of concerted atomic motion characteristic of the conformational behavior of a molecule. Of course, the interesting conformations are those of sufficiently low free energy to be populated at reasonable temperatures. 

Geometrical descriptors are derived from the three-dimensional representations and include the principal moments of inertia, molecular volume, solvent-accessible surface area, and cross-sectional areas. Since conformational analysis (see Conformational Analysis 1 Conformational Analysis 2 and Conformational Analysis 3) often requires calculation of atomic charges, these routines can also produce electronic descriptors. Electronic descriptors characterize the molecular structures with such quantities as LUMO and HOMO energies, bond orders, partial atoim c charges, etc. Hybrid descriptors combine aspects of several of these descriptor types. The design and implementation of new descriptors is one important aspect of on-going research in the area of QSPR. 

For a more extensive treatment of conformational analysis see L. F. Fieser and M. Fieser, Steroids, Reinhold, New York, 1959. 

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