Lone pairs, representation

Figure 2-51. a) The rotational barrier in amides can only be explained by VB representation using two resonance structures, b) RAMSES accounts for the (albeit partial) conjugation between the carbonyl double bond and the lone pair on the nitrogen atom. 

The representation of non-bonding orbitals on an atom again uses the concept of. T-systems, though they may have any kind of hybridization (p, sp etc.), In Figure 2-56 the three possibilities arc shown lone pairs, radicals, and orbitals without electrons can be accommodated by this eoneept. 

RAMSES is usually generated from molecular structures in a VB representation. The details of the connection table (localized charges, lone pairs, and bond orders) are kept within the model and are accessible for further processes. Bond orders are stored with the n-systems, while the number of free electrons is stored with the atoms. Upon modification oF a molecule (e.g., in systems dealing with reactions), the VB representation has to be generated in an adapted Form from the RAMSES notation. 

Figure 19.18 Schematic representation of the orbital overlaps leading to M-CO bonding (a) a overlap and donation from the lone-pair on C into a vacant (hybrid) metal orbital to form a u M <—C bond, and (b) 7T overlap and the donation from a filled d or dj orbital on M into a vacant antibonding n orbital on CO to form a tt M—> C bond.

The following model is a representation of citric acid, the key substance in the so-called citric acid cycle by which food molecules are metabolized in the body. Only the connections between atoms are shown multiple bonds are not indicated. Complete the structure by indicating the positions of multiple bonds and lone-pair electrons (gray = C, red = O, ivory = H). 

The following molecular models are representations of (a) adenine and (b) cytosine, constituents of DNA. Indicate the positions of multiple bonds and lone pairs for both, and draw skeletal structures (gray = C. red = O, blue = N, ivory = IT). 

Note that only when using the type of representation on the right do we show the lone pair explicitly. Spectroscopic measurements confirm the prediction of a trigonal pyramidal shape for NF . 

Representations showing electrons in molecules seem to suggest localisation of the valence electrons, but there are problematic issues in this regard. For example, we might ask if dioxygen has a double bond and two lone pairs on each O atom (as in Table 1.1) - a stmcture that does not reconcile with the paramagnetic nature of the substance - or a single bond and an odd number of electrons localised on each atom, as shown here ... 

Fig. 3.1 Schematic representation of the two modes of distamycin DNA complexes with putative hydrogen bonds shown as dashed lines. Circles with dots represent lone pairs of N(3) of purines and 0(2) of pyrimidines...

Figure 5.10 Representation of the formation of the lone pair in the PF3 molecule, (a) An isolated P3 + ion consisting of a P5+ core surrounded by two nonbonding electrons in a spherical distribution, (b) Three approaching F ions distort the distribution of the two valence shell electrons pushing them to one side of the P5+ core, (c) When the F ligands reach their equilibrium positions, the two nonbonding electrons are localized into a lone pair, which acts as a pseudo-ligand giving the PF3 molecule its pyramidal geometry.

The sodium and calcium salts of EDTA (ethylenediaminetetraacetic acid, Fig. 9.3.1.) are common sequestrants in food products. A three-dimensional representation of EDTA is shown in color Fig. 9.3.2. The EDTA ion is an especially effective sequestrant, forming up to six coordinate covalent bonds with a metal ion. These bonds are so named because a lone pair of electrons on a single atom serves as the source of the shared electrons in the bond between the metal ion and EDTA. The two nitrogen atoms in the amino groups and the oxygen... 

Fig. 23. Schematic representation of the group IV donor-hydrogen complex with hydrogen in AB site. The black spheres represent the group V atoms (As), the large white ones the group III atoms (Ga), the small white one the hydrogen atom and the dotted sphere the impurity. The lone pair on the threefold coordinated group V atom is not represented.

FIGURE 15. ORTEP representation of the coordination site of lead(II) in [Pt LsHCKTt] showing the gap occupied by the lone pair (cf Figure 14). Reproduced from Reference 91 by permission of The Royal Society of Chemistry... 

The final cu-bonded formulas (3.213), (3.214), and (3.219)-(3.221) bear an obvious resemblance to the usual VSEPR representations of these hypervalent species. Indeed, each cu-bonded structure has the same number of formal bond pairs (bp) and lone pairs (lp) as the VSEPR representation. Furthermore, the predicted angular geometries of the two models are essentially identical, with the linear (or near-linear) cu-bonded ligands occupying axial positions in the SN2-like trigonal bipyramidal motif. 

Figure 4.52 The leading donor-acceptor (nN->-szn ) interaction between the donor ammine lone pair and the acceptor 4s metal orbital in 22e [Zn(NH3)6]2+ (of. Fig. 4.51). (Note that the inner nodal structure of the Zn 4s orbital is absent in the effective-core-potential representation of the metal atom.)...

Although pathway 2 in the oxidation process (Scheme 2) may be considered analogous to mechanisms proposed for carbon hydroxylations catalyzed by cytochrome P-450, abstraction of an electron from the lone pair on nitrogen (pathway 1) would be a more likely first step in these types of reactions. It is reasonable to assume that the nature of substituents R, R2, and R3 would greatly influence the rate and path of reaction. The mechanistic possibilities in Scheme 2 are undoubtedly simplistic in their representation of the active oxygen species of cytochrome P-450 and are by no means comprehensive. However, these pathways do serve to illustrate.the role of radical substrate intermediates in cytochrome P-450-catalyzed reactions. More detailed analyses of mechanistic studies on these and other cytochrome P-450-mediated reactions can be found in recent reviews on the subject 49, 50, 60). 

Line representation Each line represents one bond or a lone pair of electrons. 

Since rigorous theoretical treatments of molecular structure have become more and more common in recent years, there exists a definite need for simple connections between such treatments and traditional chemical concepts. One approach to this problem which has proved useful is the method of localized orbitals. It yields a clear picture of a molecule in terms of bonds and lone pairs and is particularly well suited for comparing the electronic structures of different molecules. So far, it has been applied mainly within the closed-shell Hartree-Fock approximation, but it is our feeling that, in the future, localized representations will find more and more widespread use, including applications to wavefunctions other than the closed-shell Hartree-Fock functions. 

Figure 3. Schematic representation of the microcrystal considered in the computations/ the asymmetric unit (4 DeS residues, 5 Na ions and 16 water molecules, evidenced by heavy lines) is reproduced according to the crystallographic symmetry note the two ions and the water molecule in special position (on the diagonal 2-axis at -c/8). Hydrogen atoms in the polymer and lone-pairs are omitted in the drawing.

The study of carbon compounds provides us with the subdivision organic chemistry , and a few simple organic compounds can exempMfy this shorthand approach to molecular representations. The primary alcohol propanol (systematically propan-l-ol or 1-propanol, formerly n-propanol, n signifying normal or unbranched) can be represented by a stmcture showing all atoms, bonds, and lone pair or nonbonding electrons. 

These orbital pictures tend to get a little confusing, in that we really need to put in the elemental symbol to distinguish it from carbon, and we usually wish to show the lone pair electrons. We accordingly use a compromise representation that employs the cleaner line drawings for part of the structure and shows the all-important orbital with its lone pair of electrons. These are duly shown for ammonia and water. 

The definition of aromaticity conceived by Hiickel strictly applies to monocyclic ring systems, but indole, constructed from the fusion of benzene and pyrrole, behaves as an aromatic compound, like quinoline and isoquinoline. The ring fusion, however, affects the properties of both components. This is reflected in the valence bond description of indole, shown in Scheme 7.1, where one canonical representation shows electron density shared between N-1 and C-3 in the pyrrole unit (implying enamine character). Note that although other canonical forms can be drawn, where the lone-pair electrons are delocalized into the benzenoid ring, their energy content is relatively high and they are of limited importance. 

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