Molecular representations relative importance

Orbital Surfaces. Molecular orbitals provide important clues about chemical reactivity, but before we can use this information we first need to understand what molecular orbitals look like. The following figure shows two representations, a drawing and a computer-generated picture, of a relatively high-energy, unoccupied molecular orbital of hydrogen molecule, H2. 

Tversky [45] addressed this problem using a feature-based approach, which admits the concept of asymmetric similarities (cf. the discussion of asymmetric similarities related to Tversky s work [46]). As will be seen in the sequel, asymmetric similarities also have a role to play when comparing molecules, albeit a relatively small one currently. In a manner that is quite like that used in molecular applications of similarity, (yide infra) lists of features are used to characterize the mental representations being compared. Some type of relationship is then used to assess the similarity based on the number of features that are common and different between two representations and their relative importance. The form of the functions investigated by Tversky [45] are closely related to some of those used in molecular similarity studies (see also Sections 15.4.2-15.4.4 and Table 15.3 and Table 15.4). 

This section attempts a brief review of several areas of research on the significance of phases, mainly for quantum phenomena in molecular systems. Evidently, due to limitation of space, one cannot do justice to the breadth of the subject and numerous important works will go unmentioned. It is hoped that the several cited papers (some of which have been chosen from quite recent publications) will lead the reader to other, related and earlier, publications. It is essential to state at the outset that the overall phase of the wave function is arbitrary and only the relative phases of its components are observable in any meaningful sense. Throughout, we concentrate on the relative phases of the components. (In a coordinate representation of the state function, the phases of the components are none other than the coordinate-dependent parts of the phase, so it is also true that this part is susceptible to measurement. Similar statements can be made in momentum, energy, etc., representations.)... 

Some other systems - beside the series of relative ones - have also been studied in localized representation, using the LMBPT scheme. Some of these systems have importance in biology. Two kinds of molecular systems have been investigated, each of them is related to the CH2O molecule which is now believed to be one of the most important small molecular species in human life. 

Standardized and consistent representations of stereoisomers and stereoisomeric mixtures are similarly important for the unique representations of distinct compounds. Recent file formats such as SDF v3000 and ChemAxon Extended SMILES provide clear definition and representation of complex relative and absolute stereochemical configurations. In practice these are not widely used because many commercially available files are represented by established v2000 or SMILES formats and also because HTS compounds are mostly relatively simple low molecular weight structures. 

The existence of a charge density presupposes a concomitant set of MOs and Sect 2.3 describes how chemical reactivity can be based on the notion of Frontier Molecular Orbital (FMO) control i.e. the most important orbital interactions are between the HOMO on one species and the LUMO on the other or vice versa. FMO control, together with electrostatic charge control, provides a powerful qualitative basis for interpreting reactivity. The relative energies and compositions of MOs are vital and many computer programs now provide 3-dimensional representations of MOs to facilitate analysis. 

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