Molecule selection, equivalences

With respect to the size and charge selectivity of paracellular pathways, equivalent pore theory has been utilized to calculate an effective radius based on the membrane transport of uncharged hydrophilic molecules, while equivalent circuit theory has been used to separate mediated from paracellular membrane transport of small ions. The term equivalent should be emphasized, as selectivity parameters are obtained from membrane transport data, so phenomenological information is used to quantitate the magnitude of aqueous pathways... 

This extension does not have to be applied to all the atoms of the molecule, but to as many as chemically relevant for example in the study of interacting molecules one can select the relevant part of the atoms in the super-molecule. In equivalent fashion one can add configurations to the part of the hf-hl function, fjjp = introducing... 

Atoms have complete spherical synnnetry, and the angidar momentum states can be considered as different synnnetry classes of that spherical symmetry. The nuclear framework of a molecule has a much lower synnnetry. Synnnetry operations for the molecule are transfonnations such as rotations about an axis, reflection in a plane, or inversion tlnough a point at the centre of the molecule, which leave the molecule in an equivalent configuration. Every molecule has one such operation, the identity operation, which just leaves the molecule alone. Many molecules have one or more additional operations. The set of operations for a molecule fonn a mathematical group, and the methods of group theory provide a way to classify electronic and vibrational states according to whatever symmetry does exist. That classification leads to selection rules for transitions between those states. A complete discussion of the methods is beyond the scope of this chapter, but we will consider a few illustrative examples. Additional details will also be found in section A 1.4 on molecular symmetry. 

We now turn to electronic selection rules for syimnetrical nonlinear molecules. The procedure here is to examme the structure of a molecule to detennine what synnnetry operations exist which will leave the molecular framework in an equivalent configuration. Then one looks at the various possible point groups to see what group would consist of those particular operations. The character table for that group will then pennit one to classify electronic states by symmetry and to work out the selection rules. Character tables for all relevant groups can be found in many books on spectroscopy or group theory. Ftere we will only pick one very sunple point group called 2 and look at some simple examples to illustrate the method. 

The total electron density contributed by all the electrons in any molecule is a property that can be visualized and it is possible to imagine an experiment in which it could be observed. It is when we try to break down this electron density into a contribution from each electron that problems arise. The methods employing hybrid orbitals or equivalent orbitals are useful in certain circumsfances such as in rationalizing properties of a localized part of fhe molecule. Flowever, fhe promotion of an electron from one orbifal fo anofher, in an electronic transition, or the complete removal of it, in an ionization process, both obey symmetry selection mles. For this reason the orbitals used to describe the difference befween eifher fwo electronic states of the molecule or an electronic state of the molecule and an electronic state of the positive ion must be MOs which belong to symmetry species of the point group to which the molecule belongs. Such orbitals are called symmetry orbitals and are the only type we shall consider here. 

The Slater-Kirkwood equation (Eq. 39) was selected with N = 4 for carbon and N = 1 for hydrogen. The success of the equivalent calculation for the intermolecular interaction of CH4 molecules was mentioned in the previous section. Atoms, rather than bonds, were chosen as the basis for the calculation because the location of the atom centers is unambiguous and the approximation of isotropic polarizability is better for an atom than for a bond. Possible deviations from isotropic polarizability are discussed in Section V. Ketelaar19 gives for the atomic polarizabilities of hydrogen and carbon a = 0.42 and 0.93x 10-24 cm3, respectively. The resulting equation for the London energy is... 

The preceding section can be further generalized, to properly account for absorption of nonionized molecules. The selection of the maximum Pe for HIA prediction implicitly recognized that only a fraction of the small intestine is available for the maximum absorption of acids (with pKa near 4) and bases (with pKa near 9). But when this approach is applied to nonionizable molecules, then the absorption may be underestimated, since absorption should be uniform across the whole intestinal tract. The remedy is to sum the two Pe values. This is roughly equivalent to... 

The analysis of the histograms of photon arrival times is equivalent in both cases and relies on fitting appropriate model functions to the measured decay. The selection of the fitting model depends on the investigated system and on practical considerations such as noise. For instance, when a cyan fluorescent protein (CFP) is used, a multi-exponential decay is expected furthermore, when CFP is used in FRET experiments more components should be considered for molecules exhibiting FRET. Several thousands of photons per pixel would be required to separate just two unknown fluorescent... 

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