TP-6 and TP-7 Linear Tetrapyrroles

TP-6 Linear tetrapyrroles
TP-6.1 Fundamental system
TP-6.2 Unsubstituted oxidised bilanes
TP-6.3 Semisystematic nomenclature
TP-6.4 Trivial names
TP-6.5 Modified trivial names
TP-7 Relatives of linear tetrapyrroles
TP-7.1 Linear tripyrroles
TP-7.2 Dipyrroles
References for this section

TP-6.1. Fundamental system. The structure in Fig. 13 is called "bilane". It is defined without oxygen substituents, and is numbered (omitting C-20) to agree with the numbering of the unsubstituted porphyrin ring system (see Fig. 2). Unless otherwise specified it is implied that each nitrogen.atom of bilane (Fig. 13) is saturated.

Fig. 13. Bilane (trivial name bilinogen)

Note The use of bilane in biochemical literature is established although it does not follow the guidelines set forth in IUPAC Rule F-3. [See RF-3 in 1999 revised rules]

TP-6.2. Unsubstituted Oxidised Bilanes. Unsubstituted oxidised bilanes may be named semisystematically on the basis of the bilane structure in Fig. 13. The number of additional double bonds involving the carbon bridges is indicated by changing the ending '-ane' to '-ene' (1 such additional double bond, total 9 double bonds), and '-adiene' (2 such additional double bonds, total 10 double bonds). The system with one further double bond (total 11 double bonds) has already been defined [ref 9] as bilin (Fig. 14) and this name is used in preference to bilatriene. The location of the additional double bonds for the bilene and biladiene names is indicated by the letters a, b, or c corresponding to the bridge positions 5, 10 and 15 respectively.

Fig. 14. Bilin (22H-form drawn conventionally)

Where it is necessary to specify the stereochemistry of the 4(5)-, 5(6)-, 9(10)-, 10(11)-, 14(15)- and/or 15(16)-double bonds, it should be indicated by E or Z according to TP-0.3.

Examples:

Note The use of bilene and biladiene in biochemical literature is established although they do not follow the guidelines set forth in IUPAC Rule F-3. [See alsoRF-3 in 1999 revised rules]

1.	Bilene-a
2.	Bilene-b
3.	Biladiene-ab
4.	Biladiene-ac

The name 1,19-secocorrin (Fig. 15) defined previously [ref 9] may be used in place of 1,2,3,7,8,12,13,17,18,19-decahydrobilin. Secocorrin names are derived systematically from the corrin nomenclature.

Note IUPAC-IUB Commission on Biochemical Nomenclature, "Nomenclature of Corrinoids, Rules Approved 1975." Pure Appl. Chem. 48, 495-502 (1976).

Fig. 15. 1,19-Secocorrin (22H-form drawn)

TP-6.3. Semisystematic Nomenclature. Substituted linear tetrapyrroles may be named on the basis of the fundamental bilane structure (Fig. 13) and the less saturated systems defined in TP-6.2. The appropriate parent is selected according to the number, and location, of the C,C-double bonds involving C-5, C-10 and/or C-15. All substituents are expressed by prefixes and/or suffixes as in systematic nomenclature. Positions of substituents are determined in accord with IUPAC Rule C-15.11(b) to (e) based, where relevant, on the 22H form.

Note Common biochemical practice favors the expression of the ketone function as a suffix in contradistinction to the usual hierarchy of functions in systematic nomenclature which favors the expression of the acid function as a suffix.

Examples:

Note The linear tetrapyrrole structures shown in examples 1-5 are formally tautomeric with the corresponding bilin-1,19-diols.

Bilin-1,19-diol
However, present evidence indicates that the bislactam form predominates and most naturally occuring linear tetrapyrroles are named on the basis of the bislactam (i.e. -1,19-dione) tautomer.

1.	3,7-Bis(2-carboxyethyl)-2,8,12,17-tetramethyl-13,18-divinylbilin-1,19(21H,24H)-dione (biliverdin IXβ)
2.	2,18-Bis(2-carboxyethyl)-3,7,12,17-tetramethyl-8,13-divinylbilin-1,19(21H,24H)-dione (biliverdin IXγ)
3.	3,7-Bis(2-carboxyethyl)-2,8,13,18-tetramethyl-12,17-divinylbilin-1,19(21H,24H)-dione (biliverdin IXδ)

Note Note that the systematic orientation and numbering differ from that.accepted for the trivial name, biliverdin IXδ

4.	8,12-Bis(2-carboxyethyl)-3,7,13,17-tetramethyl-2,18-divinylbilin-1,19(21H,24H)-dione (biliverdin IIIα)
5.	8,12-Bis(2-carboxyethyl)-2,7,13,18-tetramethyl-3,17-divinylbilin-1,19(21H,24H)-dione (biliverdin XIIIα)
6.	8,12-Bis(2-carboxyethyl)-3,18-diethyl-2,7,13,17-tetramethylbiladiene-ac-1,19(21H,24H)-dione (mesobilirubin, see Fig. 19)

Note Note that the systematic orientation and numbering differ from that accepted for the trivial name, mesobilirubin.

7.	8,12-Bis(2-carboxyethyl)-3,18-diethyl-2,7,13,17-tetramethylbiladiene-ab-1,19(16H,21H)-dione (15,16-dihydromesobiliverdin, see example 1, TP-6.5)
8.	2,3,7,8-Tetraethyl-12,13,17,18-tetramethylbilane-1,19(4H,16H)-dione
9.	3,8,13,18-Tetrakis(carboxymethyl)-19-hydroxymethylbilane-2,7,12, 17-tetrapropionic acid
10.	8,12-Bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,10,19(21H,24H)-trione

TP-6.4. Trivial Names. Seven trivial names and associated locants are retained for naming the substituted linear tetrapyrroles shown in Fig. 16-22. The side chains may be numbered using the locant of the point of substitution on the bilane system with a following superscript numeral as for trivially named porphyrins in TP-2.1.

Note In the recommended nomenclature the Roman numeral and Greek letter (that in the Fischer system refer in a formal way to the substitution pattern and to the position of cleavage of the corresponding porphyrin respectively) have been dropped. Thus biliverdin was formerly biliverdin IXa. Because the vast majority of references are to this common substitution pattern, it has become common practice to drop the IXa designation.

These recommended trivial names may be used to form names for modified derivatives as directed in TP-6.5. However, positional isomers of these trivially named structures are named according to TP-6.3.

Fig. 16. Biliverdin (biliverdin IXα).

Fig. 17. Mesobiliverdin (mesobiliverdin IXα).

Fig. 18. Bilirubin (bilirubin IXα).

Note X-ray crystallography has shown that the natural compound has the configuration (4Z,15Z).See R. Bonnett, J. E. Davies and M. B. Hursthouse, Nature 262, 326 (1976).

Fig. 19. Mesobilirubin (mesobilirubin IXα).

Fig. 20. Urobilin (urobilin IXα [ref 10]).

Note If it is necessary to indicate the absolute configuration of any of the chiral centers, this should be indicated by R or S in accord with TP-0.3.

Fig. 21. Stercobilin (stercobilin IXα).

Note If it is necessary to indicate the absolute configuration of any of the chiral centers, this should be indicated by R or S in accord with TP-0.3.

Fig. 22. Urobilinogen (mesobilirubinogen IXα; urobilinogen IXα).

Note If it is necessary to indicate the absolute configuration of any of the chiral centers, this should be indicated by R or S in accord with TP-0.3.

TP-6.5. Modified Trivial Names. As an alternative to the semisystematic nomenclature of TP-6.3, substituted bilins closely related to the trivially named bilin structures shown in Figs. 16-22, in which only a few substituents differ or that differ only in degree of saturation, may be conveniently named on the basis of the recommended trivial names. The subtractive prefix "de," and the substitutive prefixes and suffixes may be used as for porphyrin derivatives in TP-3.1 through TP-3.3. When sites of saturation are known to be either one of two possible locations, the lowest possible locants are cited, followed in parentheses by the italic word "or" and the alternate locants.

Examples:

1.	15,16-Dihydromesobiliverdin (formerly mesobiliviolin IXα)

Note 1 If it is necessary to indicate the absolute configuration of any of the chiral centers, this should be indicated by R or S in accord with TP-0.3.

Note 2. Where sites of saturation are indefinite, the name would be 4,5(or 15,16)-dihydromesobiliverdin.

Note 3. Note that, in many cases, the older trivial names do not distinguish between isomeric possibilities. "Mesobiliviolin IXα" may refer to two possible isomers [ref 11].

2.	2,3-Dihydrourobilin (formerly half-stercobilin IXα)

Note If it is necessary to indicate the absolute configuration of any of the chiral centers, this should be indicated by R or S in accord with TP-0.3.

3.	10,23-Dihydrostercobilin (formerly stercobilinogen IXα)

Note If it is necessary to indicate the absolute configuration of any of the chiral centers, this should be indicated by R or S in accord with TP-0.3.

4.	2,3,15,16-Tetrahydromesobiliverdin (formerly mesobilirhodin IXα)

Note 1. If it is necessary to indicate the absolute configuration of any of the chiral centers, this should be indicated by R or S in accord with TP-0.3.

Note 2. The name "mesobilirhodin IXα" may refer to two possible isomers [ref 12].

5a.	3,31,181,182-Tetradehydro-2,3,15,16-tetrahydromesobiliverdin (phycoerythrobilin)

Note 1. If it is necessary to indicate the absolute configuration of any of the chiral centers, this should be indicated by R or S in accord with TP-0.3.

Note 2. Aplysioviolin is the monomethyl ester of this structure, W. Rüdiger, Angew. Chem., Int. Ed. 9, 473-480 (1970).

Note 3. The stereochemistry of the 3(3¹)-double bond may be indicated by E or Z in accord with TP-0.3.

5b.	4,5,181,182-Tetrahydrobiliverdin (phycoviolobilin, also known as phycobiliviolin)

Note 1. If it is necessary to indicate the absolute configuration this should be indicated by R or S in accord with TP-0.3.

Note 2. Studies on phycobiliproteins showed from the X-ray study of phycoerythrocyanin by Duerring et al. [M. Duerring, R. Huber, W. Bode, R. Ruembeli and H. Zuber, J. Mol. Biol. 211, 633-644 (1990)] and other studies of α-phycoerythrocyanin by Zhao et al. [K.-H. Zhao, M.-G. Deng, M. Zeng, M. Zhou, A. Parbel, M. Storf, M. Meyer, B. Stohmann and H. Scheer, FEBS Lett., 469, 9-13 (2000)] that, contrary to the 1986 published recommendations, phycoerythrobilin (5a) was not the same as phycoviolobilin (phycobiliviolin) (5b).

6.	3,31-Didehydro-2,3-dihydromesobiliverdin (phycocyanobilin preferred to phycobiliverdin)

Note 1. If it is necessary to indicate the absolute configuration of any of the chiral centers, this should be indicated by R or S.

Note 2. The sterochemistry of the 3(3¹)-double bond may be indicated by E or Z in accord with TP-0.3.

TP-7.1. Linear Tripyrroles. By analogy with the nomenclature of bilins, the nomenclature of linear tripyrroles is based systematically on the most unsaturated system known, which is called tripyrrin and shown in Fig. 23. Unless otherwise stated it is implied that the nitrogen atom at position 16 (e.g. in Fig. 23) is saturated.

Fig. 23. Tripyrrin

Reduced tripyrrins are named as dihydro, tetrahydro etc. derivatives:

Examples:

1.	5,15-Dihydrotripyrrin
2.	5,10,15,17-Tetrahydrotripyrrin

Note This structure is called tripyrrane in the Fischer system.

TP-7.2. Dipyrroles. It is possible to extend this nomenclature to the related dipyrrole systems, as shown below. Dipyrromethane is retained as a trivial name, and dipyrrin is introduced as a trivial name: as elsewhere in this document the names refer to systems with 2,2'-bridged pyrrole nuclei. Unless otherwise specified, it is implied that the nitrogen atom at position 11 is saturated.

Dipyrrin	(Formerly:	dipyrromethene pyrromethene)
Dipyrrin-1(10H)-one	(Formerly: pyrromethenone)
5,10-Dihydrodipyrrin Dipyrromethane	(Formerly: 2,2'-dipyrrolylmethane, dipyrrylmethane, pyrromethane)

References for this section

9. A. Eschenmoser, Chem. Soc. Quarterly Rev., 24, 366, (1970).

10. For a discussion of the confused earlier practices see T. K. With, Bile Pigments, pp. 3031, Academic Press, New York and London, 1968.

11. M. Stoll and C. H. Gray, Biochem. J., 117, 271 (1970).

12. P. O'Carra and S. D. Killilea, Tetrahedron Letters, 4211 (1970).