Molecular similarity quantum mechanical basis

The primary difference between covalent and ionic bonding is that with covalent bonding, we must invoke quantum mechanics. In molecular orbital (MO) theory, molecules are most stable when the bonding MOs or, at most, bonding plus nonbonding MOs, are each filled with two electrons (of opposite spin) and all the antibonding MOs are empty. This forms the quantum mechanical basis of the octet rule for compounds of the p-block elements and the 18-electron rule for d-block elements. Similarly, in the Heider-London (valence bond) treatment... 

The overall form of each of these equations is fairly simple, ie, energy = a constant times a displacement. In most cases the focus is on differences in energy, because these are the quantities which help discriminate reactivity among similar stmctures. The computational requirement for molecular mechanics calculations grows as where n is the number of atoms, not the number of electrons or basis functions. Immediately it can be seen that these calculations will be much faster than an equivalent quantum mechanical study. The size of the systems which can be studied can also substantially ecHpse those studied by quantum mechanics. 

Unlike molecular mechanics, the quantum mechanical approach to molecular modelling does not require the use of parameters similar to those used in molecular mechanics. It is based on the realization that electrons and all material particles exhibit wavelike properties. This allows the well defined, parameter free, mathematics of wave motions to be applied to electrons, atomic and molecular structure. The basis of these calculations is the Schrodinger wave equation, which in its simplest form may be stated as ... 

The key differences between the PCM and the Onsager s model are that the PCM makes use of molecular-shaped cavities (instead of spherical cavities) and that in the PCM the solvent-solute interaction is not simply reduced to the dipole term. In addition, the PCM is a quantum mechanical approach, i.e. the solute is described by means of its electronic wavefunction. Similarly to classical approaches, the basis of the PCM approach to the local field relies on the assumption that the effective field experienced by the molecule in the cavity can be seen as the sum of a reaction field term and a cavity field term. The reaction field is connected to the response (polarization) of the dielectric to the solute charge distribution, whereas the cavity field depends on the polarization of the dielectric induced by the applied field once the cavity has been created. In the PCM, cavity field effects are accounted for by introducing the concept of effective molecular response properties, which directly describe the response of the molecular solutes to the Maxwell field in the liquid, both static E and dynamic E, [8,47,48] (see also the contribution by Cammi and Mennucci). 

Although QS has started within such similarity-dissimilarity index premises, essentially the fact is that the elementary QS computational element building block reduces to the well-known scalar product of two DFs, a so-called similarity measure. Indeed, given two quantum systans, say [A,B), the familiar quantum mechanical theoretical basis permits to obtain their attached wavefunctions via solving the respective Schrbdinger equations. From the system wavefunctions, a pair of associated DF p,4(r),pg(r) can be simply set up, with the vector r representing some number of particle coordinates. In molecular QS studies, the usual DF chosen is the first-order one thus, vector r = (x,y,z) corresponds to one-electron position coordinate only. Then, the similarity measure between the system pair of DF is simply defined as the overlap similarity integral ... 

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