Terminology Describing Stereochemistry

In addition to the regiochemistry, there is also special terminology used to describe the stereochemistry of a reaction. As an example, consider the following simple alkene  

Suppose that we have an anti-Markovnikov addition of H and OH across this alkene  

We know which two groups are adding to the double bond, and we know the regiochemistry of the addition. But in order to draw the products correctly, we also need to know the stereochemistry of the reaction. To better explain this, we will redraw the alkene in a different way. 

The vinylic carbon atoms, highhghted above, are both sp hybridized, and therefore trigonal planar. As a result, aU four groups (connected to the vinylic positions) are 

This is an unusual way to draw an aUcene (where all bonds are shown as wedges and dashes, rather than straight lines), but this way of drawing the alkene will make it easier to explore stereochemistry. 

The vinylic carbon atoms (the two carbon atoms of the double bond, highlighted above) are both sp hybridized, and therefore trigonal planar. As a result, all four groups (connected to the vinylic positions) are in one plane. In order to discuss stereochemistry, we will rotate the molecule so that the plane is coming in and out of the page  

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Every new class of reactions (additions, eliminations, substimtions, etc.) has its own terminology for stereochemistry. As you learn each of these classes of reactions, keep a watchful eye on what terminology is used to describe the stereochemistry. Then, look at the mechanism of each reaction within each class, and try to understand how the mechanism explains the stereochemistry. 

The problems of various types in the conventional stereochemistry are highly entangled as the result of the semantic transmutation described in the preceding subsections. It is impossible to solve the entangled problems if we maintain the conventional terminology of stereochemistry. Hence, the conventional terminology should be entirely reconsidered to restructure stereochemistry. 

The terminology and notation that have been used to describe coordination compounds have been derived with one notable exception from the terms and symbols developed to describe the stereochemistry of carbon compounds. The terms ois, trans endo, exo dextro, d, D, (+) and leva, l, L (-) all have been used to describe the stereochemistry of coordination compounds in a close analogy with organic compounds (see Figure 1). As the descriptions of the chemistry and structures of coordination systems have become more varied and complex, the meanings of these terms have become less precise, as in the example of a ois or trans tricarbonyl octahedral compound (see Figure 2). The terms fao and mer were coined to indicate the facial and meridional disposition of substituted octahedral structures. 

The structures and designations of D- and L-glyceraldehyde are defined hy convention. In fact, the D- and L-terminology is generally applied only to carbohydrates and amino acids. For organic molecules the D- and L- convention has been replaced by a new system that provides the absolute configuration of a chiral carbon. This system, called the (R) and (S) system, is described in Appendix D, Stereochemistry and Stereoisomers Revisited. 

The E or Z nomenclature can also replace the older S)m-anti terminology. Compound 51 has been called sj/n-propiophenone oxime because the OH and the phenyl are on the same side of the double bond, while 52 has been called the anti isomer because these two larger groups are on opposite sides. The distinction between syn and anti depends on the size or complexity of the substituents, and that may not always be unambiguous. Moreover, many authors reserve the terms syn and anti to describe the stereochemical pathway of a reaction, not the stereochemistry of molecules. With the E or Z system, 51 is unambiguously the Z isomer, while 52 is the E oxime. 

The almost hidden but key word here is suitable. Chemical structures can be described in very many different ways using common chemical vocabulary and terminology. One can start by focusing on atoms and bonds the hybridization of atoms atomic charges the types of bonding, localized or delocalized and other quantum chemical parameters, describing local groups, stereochemistry and conformation,... 

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