Stereochemical Nomenclature System

The currently used stereochemical nomenclature systems for configurations with four or more ligands are chirality oriented, refering to rigid configurations, or their monocentric subunits. The preceding discussion demonstrates, however, that in many cases it is preferable to use a polycentric representation. 

The present discussion of isomerism in coordination compounds is not, nor was it intended to be, comprehensive and exhaustive. The examples considered are an eclectic selection, and many important systems may have been neglected through ignorance. An obvious omission is any detailed consideration of polynuclear complexes139,256"259 and it is, of course, a quite arbitrary decision not to include any consideration of organometallic species. Other neglected issues, such as the development of a truly comprehensive system of stereochemical nomenclature, are perhaps not yet capable of solution. Nevertheless, it is to be hoped that the principal factors to be considered... 

In addition to the R and S designations, compounds with two chiral centers may also be identified by stereochemical nomenclature that describes the entire system. For example, the erythro and threo nomenclature derived from carbohydrate chemistry may be employed to describe the relative positions of similar groups on each chiral carbon. Thus, the ephedrines are designated as erythro forms since the similar groups (OH and NHCH3) are on the same side of the vertical axis of the Fischer projection, and the pseudo-ephedrines are designated as threo forms since like groups are on opposite sites of the vertical axis of the projection (Fig. 10). 

In the stereochemical nomenclature of coordination compounds, the procedure for assigning priority numbers to the ligating atoms of a mononuclear coordination system is based upon the standard sequence rules developed for chiral carbon compounds (the Cahn, Ingold, Prelog or CIP rules6, see Section IR-9.3.3.2). 

Typical of this type are the geometry indicators cis-, trans-, and fac-, mer-. Note that a more elaborate but highly functional form of stereochemical descriptors exist in the nomenclature system we shall avoid its use here. 

This nomenclature system, with (8j8) and (8a) referring to the orientation of hydrogen on Cg, and the absolute stereochemical structural assignments will be used in future discussion and depiction of the necines and their chemical relatives wherever possible. Stereochemical formulations which have been used prior to this time (74-76, 98, 152) for all the pyrrolizidine alkaloid products have been necessarily arbitrary. It is now possible to employ the complete stereochemical definitions of the pyrrolizidine products (166). 

Mislow and Siegel introduced new definitions to clarify some ambiguous stereochemical nomenclature, and they restated some topicity definitions to make them consistent with the stereochemical terms. The flow chart in Figure 2.45 shows their classification for the kinds of substituents wifliin a molecule. The classification system is based on the answer to three questions ... 

Since the lUPAC nomenclature system relies totally on the pivotal concept of the parent structure to which, in a second sphere, substituents are assigned, it appeared advisable to maintain this division also for the chapters of this book. Thus, we begin with the exposition of the nomenclature rules for parent structures and, in the second chapter, proceed with the discussion of the different types of nomenclature for substituted systems, radicals, and ions in the third chapter specific classes of functional compounds are addressed, followed, in the forth chapter, by the treatment of metal organyls and, in the fifth, of carbohydrates. The concluding sixth chapter takes up once again the construction of the final names of complex compounds including isotopic modifiers and stereochemical descriptors. 

FIGURE 1.1 Chemical and stereochemical nature of amino acids. Substituents in (a) and (b) are on opposite sides of the plane N-Ca-C, the bold bond being above the plane. Interchange of any two substituents in (a) changes the configuration. For the Cahn-Ingold-Prelog system of nomenclature, the order of preference NH2 > COOH > R2 relative to H is anticlockwise in (a) = (S) and clockwise in (c) = (R). 

Although all alkaloids can be named by the principles already outlined in this article, the cumbersome nature of such names for complex ring systems makes it desirable to use trivial parent names for some large heterocyclic skeletons. It is preferable for such trivial names to refer to skeletons with no substituents (or very few), and it is often convenient for them to carry inherent stereochemical implications. The most extensive source of these names is the Chemical Abstracts Index Guide (or the Ninth Collective Index Nomenclature Manual), but the names given here do not correspond, in many cases, to those in common use, and IUPAC recommendations, when they appear, may well differ in some respects. Some of the principal skeletons listed by Chemical Abstracts are illustrated (122-130). 

The chiral identity of a molecule is included in the nomenclature of inorganic compounds, and today s comprehensive system is based upon suggestions made in 1990 in IUPAC s Recommendations on Nomenclature of Inorganic Chemistry [84], and ACS s Inorganic Chemical Nomenclature [90]. The basis for the usage of stereochemical descriptors was laid by Brown [91,92], from which three types of chiral descriptor conventions were developed (i) Steering-wheel-convention [93], (ii) Skew-lines convention [94] and (iii) Oriented-skew-lines convention [95]. 

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