RF-1 to RF-3

Contents of this section

• RF-1. Biologically Based Trivial Names
• RF-2. Semisystematic Nomenclature for Natural Products
• RF-3. Fundamental Parent Structures
  • 3.1 General Guidelines for Chosing a Fundamental Parent Structure
  • 3.2 Structural Features Allowed for Fundamental Parent Structures
  • 3.3 Semisystematic Names
  • 3.4 Indicated Hydrogen
  • 3.5 Numbering of Fundamental Parent Structures
  • 3.6 Identification of Individual Rings
  • 3.7 Stereochemical Configuration of Fundamental Parent Structures

Rule RF-1. Biologically Based Trivial Names

RF-1.1. When a compound is isolated from a natural source and a trivial name is required, the name should be based whenever possible on the family or genus or species name of the biological material from which the compound has been isolated. (Names based on a presumed metabolic activity of the isolated substance should not be generated.) As far as possible, the name should be selected to reflect the known or the likely distribution of the natural product. For example, a hypothetical species Paradigma exemplare (family Beispieliae) might yield products named on the basis of beispieliae, paradigma, or exemplare. If appropriate, the class or order might also be used as the basis for the name of a compound that occurs in a number of related families.

RF-1.2. The trivial name should not give a false implication as to structure or identity of principal groups present.

RF-1.3. The following groups of letters have significance as terminations in organic chemical nomenclature, and therefore should not be used as terminations to trivial names coined for natural products of unknown structure (except for the special case discussed in Rule RF-1.5 below).

Note: In the past, the ending -ine has been commonly used for compounds of unknown structure; however, this ending is not recommended under Rule RF-1.3 because of its significance in Hantzsch-Widman ring nomenclature (R-2.3.3.1) (ref 3).

RF-1.6. Names ending in -une or -iune are only temporary in that some unknown function and/or skeleton exists. As soon as the terminal heteroatoms and characteristic groups attached to a parent skeletal structure are identified, the ending is changed to -ane, or other suitable ending (see RF-3.3), and the terminal heteroatoms, characteristic groups, and other features should be expressed as a suffix and prefixes in the usual manner. For example, the compound paradigmune is found to be fully saturated and have an oxo and two hydroxy substituents; the name then becomes dihydroxyparadigmanone.

RF-1.7. As soon as the structure of a new natural product has been fully determined, if it is relatively simple the trivial name established above in RF-1.4 through RF-1.6 should be abandoned in favor of a systematic one based on the established principles of organic nomenclature (ref 2, 3). For a more complicated structure, if a previously known parent structure can be easily used to derive a semisystematic name for the new natural product, the trivial name should be abandoned in favor of such a semisystematic name based on the name for the established parent structure. If a previously known parent structure cannot be found, the stem name assigned above becomes that of a new parent which is numbered according to the rules given below.

RF-1.8. If it is subsequently found that the compound is identical with a known natural product structure, the trivial or semisystematic name formed later should be abandoned in favor of the previously recorded one, or a name derived systematically from it. In the latter case, the new name should be as close as possible to the one recorded earlier.

Rule RF-2. Semisystematic Nomenclature for Natural Products

Many naturally occurring compounds belong to well-defined structural classes, each of which can be characterized by a set of parent structures that are closely related structurally, that is, each can be derived from a fundamental structure by one or more well-defined operations.

RF-2.1. A semisystematic name for a naturally occurring compound or a synthetic derivative should be based on the name of an appropriate fundamental parent structure as described in RF-3.

[Examples of fundamental parent structures and names for a variety of natural compound classes are given in the Appendix.]

RF-2.2. To the name of a fundamental parent structure are added affixes denoting:

(1) modifications to the skeletal structure (RF-4, RF-6, and RF-7);
(2) replacement of skeletal atoms (RF-5);
(3) changes in the state of hydrogenation implied by the name of the parent structure (RF-8);
(4) atoms or groups substituting hydrogen atoms of the parent structure (RF-9);
(5) configurations not already implied by the name of the parent structure, or changed from that implied (RF-10). Unless specified otherwise in the rules that follow, methods of construction of the name and the principles of organic nomenclature as given in the IUPAC Organic Nomenclature Rules (ref 2, 3) are followed.

RF-3.1. General Guidelines for Choosing a Fundamental Parent Structure

RF-3.1.1. A fundamental parent structure should reflect the basic skeleton (including non-terminal heteroatoms and hetero groups) that is common to most compounds in that class.

RF-3.1.2. Fundamental parent structures should be chosen so that as many related natural products as possible can be derived from each by well-defined operations and principles of organic nomenclature.

RF-3.1.3. A fundamental parent structure should include as much stereochemistry as possible that is common to the relevant class of natural products.

RF-3.2. Structural Features Allowed for Fundamental Parent Structures

RF-3.2.1. A fundamental parent structure should only exceptionally include rings that are part of a characteristic group, such as a lactone or cyclic acetal. However, there are a number of widely used names that do include cyclic characteristic groups, for example, spirostan and cardanolide and these are allowed by these rules.

RF-3.2.2. A fundamental parent structure should not contain terminal heteroatoms or characteristic groups, except as provided by Rule RF-3.2.5.

RF-3.2.3. A fundamental parent structure should contain acyclic hydrocarbon groups that occur in most of the compounds in the natural product class.

RF-3.2.4. A fundamental parent cyclic structure should be as nearly fully saturated, or fully unsaturated in terms of the maximum number of noncumulative double bonds, as possible, while still representing the level of saturation (or unsaturation) of as many related compounds as possible. This principle should not be applied so rigorously that a large number of unsaturated bonds must be expressed by subtractive suffixes or that a large number of unsaturated bonds must be removed by hydro prefixes.

RF-3.2.5. Certain large classes of natural products, such as carbohydrates, nucleosides and peptides, are characterized by the occurrence of relatively simple but highly functionalized units and their oligomers and polymers. For these classes of compounds, called fundamental functional parents (see Introduction), the provisions of RF-3.2.2 do not apply in that fundamental parent structures may also contain functional groups.

RF-3.3. Semisystematic Name

A semisystematic name for a fundamental parent structure should be derived as far as possible from a trivial name formed according to Rule RF-1. The endings to be used in place of "-une" or "-iune" should follow the following guidelines:

(a). "-an(e)", if the entire parent structure is saturated;

(b). "-en(e)", if the cyclic or the main chain of the acyclic part, or both, of the parent structure contain the maximum number of noncumulative double bonds;

(c). "-aran(e)", if, in an otherwise fully saturated parent structure, there occur one or more individual rings that contain the maximum number of noncumulative double bonds. Most examples of such substances already have names ending in "-an" (see Note 2, below) or are alkaloids whose names end in "-ine", e.g. ergoline, aspidospermidine, and strychnidine.

Note 1: In these rules the final "e" will be used. The omission of this final "e", or the use of a final "a", may occur in languages other than English.

Note 2: The ending "-an" has been used for names of some heterocyclic parent structures having partial unsaturation, e.g. morphinan, rheadan, yohimban. Hence, even though the ending "-aran(e)" has been suggested above for structures of these types, no change to "-aran(e)" is required for names already established. However, for such compounds, the "-an(e)" ending cannot be used to indicate fully saturated analogs, which must be described using hydro prefixes (see RF-6).

Indicated hydrogen, as described in Rule A-21.6 (ref 2) and R-1.3 (ref 3), may be used to describe isomers of fundamental parent structures that have saturated skeletal atoms within a ring system or portion of a ring system having the maximum number of noncumulative double bonds.

RF-3.5. Numbering of Fundamental Parent Structures

RF-3.5.1. A numbering pattern established among a group of structurally related natural products is used for numbering the skeletal atoms of the fundamental parent structure, providing all skeletal atoms have been included in the numbering system.

RF-3.5.2. If no numbering pattern has become established among the members of a group of structurally related natural products, the fundamental parent structure is numbered according to the following guidelines:

(a) The skeleton is examined to identify a preferred ring system. This will be the ring system defined as "senior" according to the criteria of Rule C-0.14 (ref 2). The locant "1" is assigned to the atom of the preferred ring system whose locant would be "1" according to systematic numbering for that particular ring system.

(b) All skeletal atoms of the preferred ring system are assigned consecutive Arabic numbers, including atoms at fusion positions in fused ring systems, beginning with the locant "1", and following the path prescribed for systematic numbering of that particular type of ring system.

(c) Acyclic substituents to skeletal atoms of ring components or connecting acyclic structures are numbered each in its entirety, including branches, in order of the increasing value of the locant of the skeletal atom to which each is attached.

(d) Skeletal atoms of acyclic connections to other rings or ring systems, if any, are numbered consecutively beginning with the atom next to the preferred ring system, followed by the skeletal atoms of the other rings or ring systems as prescribed by (b) above; if two or more acyclic connections to other rings or ring systems are present, the one attached to the preferred ring system at the lowest numbered position is numbered first, then the ring attached to it, followed by the acyclic connector at the next lower numbered position of the preferred ring or ring system, etc.

(e) Between two groups at a gem-disubstituted position, the larger group, in terms of the number of skeletal atoms, is numbered first; if there is still a choice, the principles of Rule C-15.11(c)-(e) (ref 2) are followed. If the two groups are then identical and attached to a cyclic structure properly drawn (see Appendix) the group stereochemically α is numbered first (see RF-10.1); if the two groups are identical and attached to an acyclic terminal double bond the group trans to the main chain is numbered first as described in the carotenoid recommendations Rule 12.4 (ref 5).

RF-3.6. Identification of Individual Rings

Certain modifying prefixes for names of fundamental parent structures (see Rule RF-4) have used a ring identifier rather than specific locants of skeletal atoms. Accordingly, the identification of individual rings for some of the more common natural products has become well established. However, since in these recommendations locants of skeletal atoms are used to describe structural modifications instead of letters, except for the rather special case of removal of a terminal ring (see RF-4.6), no attempt has been made here to codify a system for lettering rings. Nevertheless, to provide continuity with the use of this system, names using letters to identify rings are given where appropriate.

RF-3.7. Stereochemical Configuration of Fundamental Parent Structures

The name of the fundamental parent structure implies, without further specification, the absolute configuration at all chiral centers and the configuration at double bonds corresponding to the group of natural products from which the parent name was derived, except as specified in these rules, or in rules for specific kinds of natural product compounds. Such stereochemistry for many fundamental parent structures is shown by the drawings in the Appendix. In some instances the configuration at a center is not implied by the parent name and must always be specified.

2. International Union of Pure and Applied Chemistry, Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F, and H, l979 edition, Pergamon Press, Oxford, 1979.

3. International Union of Pure and Applied Chemistry, A Guide to IUPAC Nomenclature of Organic Compounds, Blackwell Scientific Publications, Oxford, 1993. [Corrections see Pure Appl. Chem., 71, 1327-1330 (1999).]

5. International Union of Pure and Applied Chemistry and International Union of Biochemistry, Commission on Biochemical Nomenclature, "Nomenclature of Carotenoids", Pure Appl. Chem., 41, 405-431 (1975).