Sigma MOs

Table 3.7 shows that the photoelectron was indeed removed from the formal nc NBO (crudely equivalent to the HOMO or 5-sigma MO of the parent neutral species), whose occupancy has been reduced to 0.0346 in the cation. However, an interesting switch in the hybridization at carbon (from sp2 6 to sp0 4) has evidently altered the form of the (3-aco spin-NBO relative to the corresponding (Tco of the parent neutral species (Table 3.4(b)). 

While the sigma nonbonded interaction of lone pairs is ambiguous, the situation improves when one considers nonbonded interactions of sigma bonds. This is illustrated by reference to the molecule 1,3-butadiene. The orbitals of the C-C coupling unit are assumed to be the same as the ones shown in Fig. 11 for the C-C coupling unit of 1,2-difluoroethylene. The sigma MO s of the CH2 group and the... 

Fig. 14. Sigma fluorine lone pair interactions with the AO s of the carbon atom in F2CH2. A similar diagram can be drawn if the sigma MO s of the CH2 are considered...

Fig. 15. Sigma fluorine lone pair interactions with the sigma MO s of the C=C fragment...

Fig. 19. The sigma group MO s spanning the substituents in 1 fluoropropane as constructed from the sigma MO s of a CH bond and the fluorine sigma lone pair AO. Net stabilization results due to the Fpx-4>2 interaction...

We shall first illustrate how the OEMO approach can be used to elucidate the effect of geminal interactions on the stability and shape of molecules. We shall utilize the molecule H20 as the model system and compare the relative stabilization of the linear and bent geometries. The analysis involves the construction of the sigma MO s of H20 from the AO s of O and the group orbitals spanning the two hydrogens. 

At this point, the reader may wonder whether our prediction of the greater variation of AEpq is somewhat arbitrary. However, it must be realized that the decrease in AEpq is the result of two combined effects, i.e. a lowering of the vacant sigma MO and the simultaneous raising of the lone pair AO as A1 is replaced by A2. Typical calculated AEpq values are shown in Table 29. It can be seen that the variation is large. 

This view of a sigma MO is perpendicular to a line through the two nuclei—that is, perpendicular to the internuclear axis. A plane that cuts the MO perpendicular to the internuclear axis appears as a line in this perspective. 

DNA polymerase I, Klenow Fragment, EXO(-) was obtained from Funakoshi (Tokyo, Japan). Luciferase, Adenosine-5 -triphosphate sulfurylase, adenosine 5 -phosphosulfate sodium salt, D-Luciferin sodium salt, and magnesium acetate Tetra hydrate were obtained from Sigma (MO, USA). Deoxynucleotide and 2 -deoxyadenosine 5 -0-(l-thiotriphosphate) were obtained from Amersham Pharmacia Biotech (UK). Other chemicals were of an analytical-reagent grade. Instruments ... 

Figure 2. Molecular orbital energy diagrams for (a) FI2 showing both electrons in the bonding sigma MO and (b) Fle2 in which two of the electrons are in the antibonding sigma-starred MO...

Figure 3. Combination of p atomic orbitals to form (a) sigma MOs by end-to-end interactions or (b) pi MOs by sideways interaction.

Double or triple bonds involve two or three pairs of bonding electrons. Single bonds are always sigma bonds, but in multiple bonds the first bond is sigma, while any second or third bonds are pi bonds. The overlap of p orbitals can yield either pi or sigma MOs, as shown in Figure 3. When they overlap end to end, they form sigma orbitals, but when they overlap side to side, they form pi orbitals. 

So far we have considered only cases in which the only important MO s are formed by overlap of an s orbital on each of the two atoms. MO s of this type are called a sigma) MO s and the property that so classifies them is their cylindrical symmetry about the internuclear axis. That such symmetry must exist should be clear from the fact that each of the two s orbitals composing them is symmetrical about this axis. 

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