Compounds representation conventions

As a starting point in the description of the solid intermetallic phases it is useful to recall that their identification and classification requires information about their chemical composition and structure. To be consistent with other fields of descriptive chemistry, this information should be included in specific chemical and structural formulae built up according to well-defined rules. This task, however, in the specific domain of the intermetallic phases, or more generally in the area of solid-state chemistry, is much more complicated than for other chemical compounds. This complexity is related both to the chemical characteristics (formation of variable composition phases) and to the structural properties, since the intermetallic compounds are generally non-molecular in nature, while the conventional chemical symbolism has been mainly developed for the representation of molecular units. As a consequence there is no complete, or generally accepted, method of representing the formulae of intermetallic compounds. 

From this description, however, alternative (and/or complementary) presentations of the structure and different symbolic representations can be deduced. These are often differently defined for specific groups of compounds and may be useful to obtain a clearer view of the atomic assembly and/or to make an easier comparison between different compounds. In other words it must be underlined that there is no ideal way of describing all structure types. The most appropriate way of description depends on the structure itself but also on a number of points we are interested in emphasizing (comparison with other structural types, comparison with other compounds of the same element, etc.). These points will be discussed in a few subsequent sections after the presentation of the conventional description. 

Figure 9.1—Conventional representation of a lH NMR spectrum of an organic compound. Spectrum of butanone [CH1(C=0)CH2CH1] Superimposed is the signal integration that allows the relative areas of each type of proton present in the spectrum to be determined. The meaning of the abscissa will be explained further on.

Figure 16.1—Bar (fragmentation) spectrum and mass spectrum presented in graphical and tabular form. a) Bar spectrum of methanol b) non-conventional representation of the same spectrum in the form of a circular diagram for each 321 ions formed, there are statistically 100 ions of mass 31 u (Da), 72 of mass 29 u, etc. The various ions constitute different populations c) part of a high-resolution recording of compound M with two ions with very close m/z ratios (one due to loss of CO and the other due to loss of C2H4).

One critical task of any compound registration system is to make sure molecular structures are compliant with chemistry conventions. This ensures consistent representations of molecular structures in the database so that structure searches can find, and only find, the right compounds. Although different organizations may have slightly different conventions, the following ones are some of the most common that the Chemistry Intelligence API takes care of. 

In such representations the convention is to assume a carbon atom at each apex of the ring and that the carbon valency of 4 is made up by the appropriate number of hydrogen atoms, which are not shown explicitly A similar convention is used to simplify the writing of the structure of noncyclic compounds as well, as illustrated in some of the examples below. 

Skeletal formula The representation of an organic compound s carbon-to-carbon bonds by lines. A single line represents a single bond with double and triple lines for double and triple bonds, respectively. The carbon-to-hydrogen bonds are assumed but not shown apart from the outline, but other functional groups or elements use their conventional representation. 

Similar representations may be drawn for the open-chain structures of the other compounds, and the (i ,S)-convention applied. 

There are no formal rules for the representation of chemical compounds, although a few special cases such as steroids and carbohydrates have evolved a preferred style. This chapter will outline the revised drawing conventions used in the Combined Chemical Dictionary (CCD) (see Section 1.2.1), which other chemists may wish to follow. (CCD diagrams have, however, been added continuously over a period of nearly thirty years. This description is of best current practice.) These rules, when followed, will result in a drawing style that is consistent and unambiguous to the reader. 

There is no settled convention for the representation of polyacetals and other complex cyclic derivatives of carbohydrates. To facilitate the comparison of polycyclic derivatives of carbohydrates with alicyclic compounds, the carbohydrate derivatives will be drawn in perspective, with single rings and fused rings placed in the plane of the paper, and with darkened or broken lines used to show the orientation of substituents and bridges above or below the plane of the rings, respectively, as is customary for terpenes and steroids. 

Resonance theory (Sections 2.4-2.5) accounts for the stability and properties of benzene by describing it as a resonance hybrid of two equivalea forms. Neither form is correct by itself the true structure of benzene is somewhere in between the two resonance forms but is impossible to draw with our usual conventions. Many chemists therefore represent benzene by drawing it with a circle inside to indicate the equivalence of the carbon-carbon bonds. This kind of representation has to be used carefully, however, because it doesn t indicate the number of w electrons in the ring. (How many electrons does a circle represent ) In this book, benzene and other aromatic compounds will be represented by a single line-bond structure. We ll be able to keep count of jr electrons this way, but we must be aware of the limii tions of the drawing. . 

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