Unique and Unambiguous Specification of Stereoisomerism about a Double Bond in Nomenclature and Other Notation Systems

Abstract

In a previous communication, rules for unambiguous specification of stereoisomerism about a double bond using the descriptors E and Z were reported. These rules have been complemented to permit the derivation of a unique set of configurational descriptors for a compound. Use of these descriptor sets with chemical nomenclature and other forms of constitutional description of a compound is discussed.In a previous paper ( I ) a set of rules was described which permits unambiguous specification of stereoisomerism about a double bond employing the configurational descriptiors E and 2. The purpose of this paper is to report the extension of these rules to permit the derivation of a unique set of configurational descriptors for each compound which contains one or more stereogenic ( 2 ) double bonds. The descriptor E or 2 is assigned to each such double bond using Rules I and I1 ( I ) . Three additional rules, 111-V, provide for the derivation of the unique descriptor set for each compound. RULES FOR SPECIFYING CONFIGURATIONS ABOUT DOUBLE BONDSE and 2 are defined as follows:

Recommendations for the presentation of NMR structures of proteins and nucleic acids

“…Table 1. Pseudoatoms for the common amino acids and nucleotides used in the determination of structures of proteins and nucleic acids from NMR data [28].…”

“…For example, the ring carbons of Phe and Tyr lying in the plane with the smaller χ 2 torsion angle are designated as C δ1 and C ε1 . Indicated for reference in parentheses are the pro-R/pro-S designations for prochiral tetrahedral groups (with only the pro-R indicated as 'R') [25,26] and the E/Z designations for planar groups [27,28]. signments relative to the χ 2 torsion angle is needed to define the specific atom designators 1 and 2.…”

Stereoisograms for three-membered heterocycles: II. Chirality, RS-stereogenicity, and ortho-stereogenicity on the basis of the proligand-promolecule model

“…This differentiation is akin to the cis/trans-isomerism of double bonds, so that the system of assigning E/Z-descriptors to double bonds [27][28][29] can be extended to develop such a system of notation for specifying geometrical configurations of three-membered heterocycles.…”

Nomenclature

“…The IUPAC Commission on Nomenclature of Organic Chemistry has had continuing responsibility for revising and expanding the rules that appeared in the Definitive Report (73) (71,74,75). These revisions are often based on other significant contributions, such as for organosilicon compounds (80), organophosphorus compounds (12), and stereochemical configuration (81,82). The Hantzsch-Widman system for naming heterocyclic rings has been revised (83); nomenclature of ions and radicals (84), nomenclature for fused ring and bridged fused ring systems (85), and basic terminology of stereochemistry (86) have been dealt with comprehensively.…”

“…For the increasingly small number of organic structures that the program cannot handle, failure is explicitly indicated. It handles (R/S) stereochemical configurations (81) and topological (E/Z) configuration at double bonds (82). Early work on the reverse operation, the generation of a structure from a systematic name was carried out at the University of Hull (99).…”