Stereochemistry notation

Stereochemistry can also be expressed in the SMILES notation [113]. Depending on the clockwise or anti-clockwise ordering of the atoms, the stereocenter is specified in the SMILES code with or respectively Figure 2-78). The atoms around this stereocenter are then assigned by the sequence of the atom symbols following the identifier or (g). This means that, reading the SMILES code from the left, the three atoms behind the identifiers ( ) or ( )( )) describe the stereochemistry of the stereocenter. The sequence of these three atoms is dependent only on the order of writing, and independent of the priorities of the atoms. 

Figure 2-78. The stereochemistry of (2R,3 ,5 )-2-hydroxy-3,5-heptadiene nitrile can be expressed in the SMILES notation with or (back)slashes.

Stereochemistry can be represented graphically in 2D structures, but also by (permutations) descriptors. It is included in all line notations and exchange formats. 

The Cahn-Ingold-Prelog R-S notation has been extended to chiral allenes and other molecules that have a chiral ity axis Such compounds are so infrequently encountered however we will not cover the rules for specifying their stereochemistry in this text... 

Double bonds m the mam chain are signaled by the ending enow acid and their position IS designated by a numerical prefix Entries 6 and 7 are representative carboxylic acids that contain double bonds Double bond stereochemistry is specified by using either the cis-trans or the E-Z notation... 

Fischer projections and d-l notation have proved to be so helpful m representing carbohydrate stereochemistry that the chemical and biochemical literature is replete with their use To read that literature you need to be acquainted with these devices as well as the more modern Cahn-Ingold-Prelog R S system... 

Fischer projections and d-l notation are commonly used to describe car bohydrate stereochemistry The standards are the enantiomers of glycer aldehyde... 

Peanut oil, composition of, 1062 Pedersen, Charles John, 666 Penicillin, discovery of, 824-825 Penicillin V, specific rotation of, 296 stereochemistry of, 321 Penicillium notation, penicillin from. 824... 

See Addendum I in G. N. Burkhardt, Arthur Lapworth and Others, typescript in Robert Robinson papers, Library of the Royal Society of London. Students preparing the diplome d etudes superieures in chemistry at the Ecole Normale Superieure in the 1920s were asked to discuss questions in the oral part of the juried examination. Topics included catalysis, stereochemistry of salt complexes, and the origins of atomic notation. See bound copy of examination memoirs, presented to Albert Kirrmann, in archives of Ecole Normale Superieure Laboratoire de Chimie. 

PN and Parent Exo PX) have unsubstituted norbornenyl rings and differ from each other only in the stereochemistry of their ring fusion. These compounds have been elaborated by the incorporation of either a phenyl (tf>) or a carbomethoxy (C) group in the bridgehead (B) or vinyl (V) positions. Thus, the notation VN represents PN with a phenyl substituent at a vinyl position, while CBX represents PX with a carbomethoxy substituent at the bridgehead position. The isomerization and polymerization chemistry of these nine compounds (PN, PX, 4>BN, (jiVN, (jiVX, CBN, CBX, CVN, CVX) are the main concerns of our work. 

Notation (I) and (II) indicates two different isomers of unknown stereochemistry. 

The g subscripts are appropriate only for oaahedra] stereochemistry. The (F) and (P) notations designate the free ion term from which the listed term originates. 

The simplest names for mononuclear compounds list the ligands followed by the name of the central atom and indicate only composition. The bonding of the ligand to the central atom can be indicated by the notations given in Section 3.2.3. The stereochemistry of mononuclear compounds can be given by the notation developed in Section 3.8. For examples see Tables 11, 12 and 13. 

The enantiomers shown are related as a right-hand and left-hand screw, respectively. Chiral allenes are examples of a small group of molecules that are chiral, but don t have a chirality center. What they do have is a chirality axis, which in the case of 2,3-pentadiene is a line passing through the three carbons of the allene unit (carbons 2, 3, and 4). The Cahn-Ingold-Prelog R-S notation has been extended to chiral allenes and other molecules that have a chirality axis. Such compounds are so infrequently encountered, however, we will not cover the rules for specifying their stereochemistry in this text. 

Stereo-chemistry has played a large role in attempting to understand the visual process. While its role in the actual chromophores of vision appears to be negligible, the stereochemistry of other retinoids is widely discussed. However, many different systems of notation have been used over the years. Goodwin provides a broad review of this terminology39. 

To examine the stereochemistry of the SE process, we use the conformational notation. The intermediate 55 is formed by attack of an electrophile on the 77-system. Not all of the possible conformations of... 

Section 3, p. 36). Also, the theoretical definition does not specify the stereochemistry of the products, which are very rarely (if ever) found to be the 50/50 mixture of inverted and retained configurations predicted by classical theory (Doering and Zeiss, 1953 Okamoto et al., 1975a, b Bone et al., 1975). We shall use the term Sn 1 to refer to mechanisms in which k j is rate determining and the term classical SN 1 to refer to the mechanism (possibly defunct) in which rate-determining formation of a free carbocation is envisaged. However, kx (Fig. 2) is only rate determining if k2 > k l when internal ion pair return is important (k2 < k x) a more complex mechanistic notation is required (e.g. for solvolysis of t-butyl chloride in trifluoroethanol, p. 36). 

The structures shown in Figure 3.5 can give rise to 32, 2,048, and 512 different stereoisomers, respectively, and do not accurately represent the chemical names displayed below. It is very common that the representation of stereochemistry for both amino acids and steroids is not reported in publications. Caution must be used with the generation of the N2S engine structure dictionary from representations that omit stereo configurations, for example, from nonstereo SMILES notation. 

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