Representations of Organic Compounds

As illustrated earlier, the bonds in organic structures are represented by lines. Often, some or all of the lone pairs of electrons are not represented in any way. The reader must fill them in when necessary. To organic chemists, the most important atoms that have lone pairs of electrons are those in groups VA, VIA, and VIIA of the periodic table N, O, P, S, and the halogens. The lone pairs on these elements can be of critical concern when writing a reaction mechanism. Thus, you must remember that lone pairs may be present even if they are not shown in the structures as written. For example, the structure of anisole might be written with or without the lone pairs of electrons on oxygen  

Other possible sources of confusion, as far as electron distribution is concerned, are ambiguities you may see in literature representations of cations and anions. The following illustrations show several representations of the resonance forms of the cation produced when anisole is protonated in the para position by concentrated sulfuric acid. There are three features to note in the first representation of the product, 1-14 (i) Two lone pairs of 

Similarly, there are several ways in which anions are represented. Sometimes a line represents a pair of electrons (as in bonds or lone pairs of electrons), sometimes a line represents a negative charge, and sometimes a line means both. The following structures represent the anion formed when a proton is removed from the oxygen of isopropyl alcohol. 

All three representations are equivalent, though the first two are the most commonly used. 

A compilation of symbols used in chemical notation appears in Appendix B. 

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There have been attempts to apply formal methods to the representation of organic compounds [1],[2], some attempts to apply artificial intelligence to organic synthesis [3],[4], and numerous attempts to apply the use of molecular orbital calculations to the verification of the validity of compounds in the synthesis route. This effort was a moderate attempt to examine the representation issues involved in writing production rules for Diels-Alder disconnections. 

Line structure (2.6) Visual representation of organic compounds in which carbon atoms and the hydrogen atoms attached to them are not shown explicitly. 

The representation of organic compounds is discussed in more detail in Chapter 10. 

Fig. 13 Representation of the sorption of organic compounds to two forms of sediment organic matter, amorphous organic matter and black carbon (BC), and its effect on bioavailability...

Yan, a. and Gasteigee, J. Prediction of aqueous solubility of organic compounds based on a 3D stmcture representation. /. Chem. Inf. Comput. 

Molecular representations and functional groups in organic compounds, (a) Different ways to represent the structures of aliphatic and aromatic compounds, (b) Some important functional groups attached to organic skeletons, and the corresponding names of organic compounds. 

Figure 9.13—Effect of resonance on carbonyl-containing compounds. Representation of the delocalisation of valence electrons in mesomeric forms of organic compounds. In1 C NMR, the signal corresponding to a carbonyl in an ester is at 165 ppm, whereas it is at 205 ppm for a ketone.

Yan, A., J. Gasteiger, M. Krug, and S. Anzali. 2004. Linear and nonlinear functions on modeling of aqueous solubility of organic compounds by two structure representation metdoCtomput. Aided Mol. Des 18 75-87. 

Figure 16 Schematic representation of the reaction pattern for the oxidation of organic compounds with simultaneous oxygen evolution at metal-oxide anodes reactions (a), (b), (c), d) as in Figure 11 (e) combustion of the organic compound R via electrochemical oxidation mediated by physisorbed hydroxyl radicals (/) selective chemical oxidation of the organic compound at the higher metal oxide surface sites. (From Ref. 15. Copyright 1994, Pergamon Press Ltd. Reprinted with permission.)...

In valence bond terms, the isonitrile (isocyanide) group requires representation as two resonance structures (140a) and (140b), but physical properties indicate that the dipolar contribution (140a) is the major one. The isonitrile structure involves divalent carbon, a property shared only with carbon monoxide and fulminates (R—O—NC) as isolable entities. Since the latter are notoriously reactive materials, this singles out the isonitriles as the only stable family of organic compounds which are formally divalent. 

Reasonably accurate (agreement with literature values better than 5%) heats of evaporation of some solvents (water, ether, dioxane) and NH4N03 solutions were obtained by TG methods (99). This technique also was used (100) to study the volatilization rates of some organic compounds that are of interest as environmental contaminants (naphthalene, hexachlorobenzene, 4-chlorobiphenyl, n-decane). Evaporation rates were influenced by the rates of heating (5, 10, and 25 K min-1)-A good representation of behavior was provided by the evaporation model, described in detail, provided that the surface area of the substance was known. It was assumed that equilibrium was established between condensed phase and vapor and that there was convective transport and diffusion to the container outlet. It was concluded that TG methods provide a useful method for studies of the evaporation of organic compounds. 

In 1859 Kekule started to use graphical representations of organic molecules, in part to emphasize the tetravalent nature of carbon atoms and their ability to form chains. He then turned his attention to the structure of benzene (CsHg), a compound with unusual properties that could not be explained by any theories of the day. 

A further limitation of the CENTURY phosphorus model is the lack of an explicit representation of the impact of soil enzymes on the mineralization of organic phosphorus compounds. The results presented in this book indicate that there is limited data with which to quantify the relative importance of enzymatic hydrolysis of organic phosphorus [biochemical mineralization) vs. organic phosphorus mineralization associated with the decomposition of organic compounds [biological mineralization). It is very difficult to develop models that include enzymatic mineralization of organic phosphorus without data to quantify the relative importance of this process. 

Figure 4.4 Schematic representation of the two-film model for the distribution of organic compounds between air and water.

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