Intern:Hopanoids in PANGAEA

This is a work in progress page. Hopanoid lipids are commonly used biomarkers and molecular clocks for evolutionary times ("molecular fossils").

=Definition= More detailed description follows.

Hopanoid lipids play a similar role in prokaryots, as sterol lipids (e.g. cholesterol) do in eukaryots. Hopanoids are mainly found in bacteria, but can also be found in some plants.

The differences and similarities between hopanoids and sterol lipids are listed in the following table: Hopanoids can be seperated into two groups:

Biologically produced hopanoids (=biohopanoids)

Abiotically matured hopanoids (=geohopanoids, representing molecular fossils)

=Short rules at a glimpse=
 * Greek symbols shall be used for α/β-isomerism in parameter names
 * Locants shall be given for α/β-isomerism
 * A capital "(H)" is added right after the letter α/β in α/β-isomerism in order to refer to hydrogen if it helps to avoid ambiguity (e.g. 21α(H))
 * No number of carbon-atoms is neccessary for homohopanoids, use numerical prefixes (homo-, bishomo, trishomo) instead
 * If double bonds do not lie between two consecutively numbered carbon-atoms, add the higher locant in brackets after the lower locant (e.g. hop-22(29)-ene)
 * Loss of carbon atoms are indicated with the locant of lost carbon atoms and the prefixes nor-, bisnor-, trisnor- etc.

=Nomenclature of hopanoids=

Projection of hydrogen atoms
Because of the planarity of the hopanoid-ring-system and consequently the existence of two molecule faces, hydrogen atoms can be projected in two directions with regard to the plane. Thus, two stereoisomers exist. The α/β-face nomenclature describes these molecule configurations (Rose et al., 1980, Chapter P-101.2.6 in IUPAC 2013).

Two such stereocenters with natural occuring α/β-isomers exist for hopanoids: C17 and C21. Due to the counterclockwise numbering of hopanoids, the face shown in standard visualisation represents the β-face. Consequently:


 * For α-isomers, the hydrogen atom projects into the plane
 * For β-isomers, the hydrogen atom projects towards the viewer

Many scientists tend to shorten molecule names, so that locants of α-/β-isomers are ommited. Please note, that PANGAEA discourages this shortening and encourages scientists and curators to use the full-description including locants as well as to refer to the hydrogen as (H). The addition of "(H)" to the locant shall underline, that the isomerism refers to the projection of hydrogen in order to avoid ambiguity, especially in position C-21 (position of side-chain-attachment). Location C-17 is treated likewise for uniformity, although not mandatory.

The recommended full descriptions are listed in this table:

Please note, that the addition of "(H)" is otherwise only neccessary, if:
 * Two substituents (one being hydrogen) can project up- or downward and the hydrogen-substituent is determining the direction of the other (e.g. if Hydrogen is α, the X must be β)


 * The substituent can not be named as prefix seperately, because it is included inside another name-compartment (e.g. due to cyclization as descriped in P101.3.3,IUPAC 2013)

Although IUPAC nomenclature prefers to put the whole locant into brackets, if the hydrogen symbol "H" is involved (e.g. "(17αH)"), the spelling "17α(H)" has been widely adopted. This is the reason, why PANGAEA differs from the IUPAC recommendations in this point.

Care should be taken, not to confuse the "(H)" symbol of α/β-isomerism with indicated hydrogen.

Projection of functional groups
As for hydrogen-atoms, other functional groups, e.g. hydroxyl-groups or methyl-groups, can be projected into the plane or towards the viewer. The rules are the same as for hydrogen. The letter α or β respectively is added right after the locant, before the pre- or suffix e.g. "2β-methyl-(...)" or "(...)-11α-ol.

Fundamental parent structures
"Hopane" has become a retained name, recognizing it as fundamental parent structure. This allows for contruction of semisystematic names, which simplify the nomenclature of hopanoids tremendously in comparison to full systematic names working with fused-ring-system-naming. Some examples are listed in the following table:

It should be noted, that these parent structures contain information about a specific configuration. Therefore, the standard configuration is assumed, if not otherwise stated. According to rule P-101.2.6 in IUPAC 2013, only configurations, that differ from the parent structures, need to be stated.

ββ-isomers are naturally occuring isomers, other configurations are created by maturation within the sediment (reference).
 * hopane =  17β(H),21β(H)-isomer

Double bonds
The normal rule for assigning locants to double bonds, is described in (reference neccessary)

However for polycyclic compounds like hopanoids, double bonds may not lie two consecutively numbered atoms. For showing the direction of the double bond, the lower C-atom-locant is given followed by the connecting C-atom-locant in brackets e.g. in hop-20(29)-ene (double bond between C-20 and C-29). (reference neccessary)

Loss of carbon atoms
The loss of carbon atoms (commonly methyl-groups, no ring-contractions) from the base-structure of hopanoids is described using the prefix "nor-". For loss of multiple carbons, the prefixes "bisnor-", "trisnor-" etc. are used.

Please note, that the numerical multipliers "di-", "tri-" etc. are not used in this case, although other compound classes (steroids e.g. cholesterols) prefer these in combination with the "nor"-prefix. (reference needed)

Size of homohopanoids
The total size (amount of carbon atoms) of homohopanes is given by numerical multipliers in front of the "homo"-prefix (see also here): According to IUPAC Nomenclature of Steroids (1989), non-detachable prefixes like "homo" are preferred to detachable prefixes like "methyl" (rule 38-6.3. b)), which is why the side-chain is not mentioned in a substitutive way.
 * hopane = C30
 * homohopane = C31
 * bishomohopane = C32
 * trishomohopane = C33
 * tetrakishomohopane = C34
 * pentakishomohopane = C35

Please note, that the numerical multipliers make the addition of number of carbon atoms to PANGAEA parameter names obsolete!

Example: "C33 22S 17α-21β trishomohopane" can be shortened to "(22S)-17α(H),21β(H)-trishomohopane"

The locants of methylene-group (-CH2-) addition is often omitted, however, following chapter P-101.3.2.1 (IUPAC, 2013) and rule 3S-6.1. (IUPAC Nomenclature of Steroids, 1989), the locants of added methylene groups (=locant of attachment + letter a,b,c...) should be given in front of the prefix. However this is not common practice for hopanoids.

Some scientists instead only state the locant of the point of attachment (i.e. C-29 for the side-chain), however this is neither recommended by IUPAC.

Chirality of homohopanoids
The C22-position of the hopanoid base structure is prochiral (see prochirality in IUPAC gold book). A chiral center is characterized by sp3-hybridization of the C-atom (tetrahedral), carrying four different substituents causing the molecule to be either a left- or right-handed mirror-image. This happens oppon side-chain formation of homohopanoids.

Chirality of bacteriohopanepolyols
The carbon-centers of hydroxyl-group attachment are chiral and can thus either be R- or S-configurated. Please note that the R-/S-designation of the same carbon atom may change for long semisystematic names upon further substitution, although the spatial orientation of substituents remains the same. The reasons lie within the Cahn–Ingold–Prelog priority rules, which mainly work with atomic numbers to determine priorities. Further substitutions of the side-chain (e.g. further hydroxylation) may change priorities and consequently R-/S-designations.

Example (pay attention to C22 and C33):


 * (22R,32R,33R,34S)-17β(H),21β(H)-35-aminobacteriohopane-32,33,34-triol
 * (22S,30R,31R,32R,33S,34S)-17β(H),21β(H)-35-aminobacteriohopane-30,31,32,33,34-pentol

Hydroxylation of hopanes
There are different groups of hydroxylated hopanoids.

Bacteriohopanepolyols are very specific compounds, that are basically pentakishomohopanes (C35) with 22R-configuration and 17β,21β-projection of hydrogen-atoms. The hydroxyl-group-configuration is also well defined. Therefore, locants and descriptors are usually omitted. For more information, please read the corresponding chapters of this wiki-page.

Hopanols in general are a more divers group. Although bacteriohopanepolyols belong to the bigger group of hopanols, they also include hopanes with hydroxylation of the ring-system and shorter side-chains. Different stereoisomerism is also more common. However, if not otherwise stated (and except for "hopanol"), the position of the hydroxyl-group is also assumed to be located at the terminal side-chain atom. Please note, that not all hopanols occur naturally. Many terminal-side-chain hydroxylated hopanols are chemically altered bacteriohopanepolyols, which would otherwise not be easily analysable due to their high polarity (compare Talbot et al. 1, Talbot et al. 2, Kool et al.)

Neohopanes
Neohopane is a parent structure, for which the hydrogen at C17 and the methyl-group at C18 are exchanged (reference needed). The projections of hydrogen and methyl are the same however as for hopane.

Benzohopanoids
Benzohopanoids are products from chemical alteration of bacteriohopanepolyols during diagenesis.

The side-chain can cyclisize either at C-16 or C-20. Cyclisation at C-16 requires at least one additional side-chain carbon (connection between C-16 and C-31), at C-20 at least two additional side-chain carbons (connection between C-20 and C-32). Spare carbon-atoms make up for the rest (R) attached to the benzene-moiety.

For semisystematic names, PANGAEA adheres to the recommendations by Rybicki et al. to depict the cyclisation as prefix and add unsaturation of bonds as suffix according to the usual rules: An alternative semisystematic nomenclature created by Schäffer et al. exists using "benzo" as prefix followed by square-brackets citing the attachment site locants. This leads to the neccessity of using the nor-prefix to eliminate the side-chain. However because this nomenclature does not follow IUPAC rules properly, this nomenclature is inadvisable.
 * 16,31-cyclo(...)16,21,30-triene
 * 20,32-cyclo(...)20,22(30),31-triene

In addition to cyclisation of the side-chain, benzohopanoids may contain unsaturations of existing hopanoid-ring-structures creating further benzene-moieties. This can be semisystematically described using the nor-prefix (for lost methyl-groups due to unsaturation) and common rules for the "ene"-suffix.

Total carbon-counts can not be used to conclude the base structure of benzohopanoids (as it is possible for simple homohopanoids).

Hopanoic Acids
Hopanoic acids are degradation products of bacteriohopanepolyols during diagenesis (reference). If not otherwise stated, the carboxyl-group is situated at the terminal end of the side-chain. Trivial names therefore often omit locants, however it is recommended to use semisystematic names including all known information.

Example:

bishomohopanoic acid = 17β(H),21β(H)-bishomohopan-32-oic acid

Homohopanoids
Homohopanoids are hopanoids carrying a side chain in position C22. These plain side-chains have not been produced naturally by bacteria but due to sediment maturation. During diagenesis, bacteriohopanepolyols become defunctionalized under anaerobic conditions (reference).

Adenosylhopanes
tbc

Bacteriohopanepolyols
tbc

Bacteriohopanepolyol cyclitol ether
tbc

Aminobacteriohopanepolyols
35-aminobacteriohopanepolyols are characteristic BHPs of methanotrophs (reference). The amino-group of aminobacteriohopanepolyols is situated at the terminal side-chain carbon atom C-35. Locants are therefore often omitted in trivial names. Some trivial names are even further shortened to "aminotriol", "aminotetrol" and "aminopentol" respectively.

=Information ressources and databases=
 * Hopanoids information at Lipidhome/Lipidweb
 * Hopanoids [PR04 in Lipid Maps Structure Database (LMSD) ]
 * Wiki-page about hopanoids
 * Campro Scientific brochure about C31-C35 homohopanes, brochure overview
 * Campro Scientific brochure about C30-hopanes, brochure overview
 * Sigma Aldrich Analytix Journal Volume 6 Article 5 about hopanoid nomenclature
 * The Lab Summons article on hopanoid stereoisomerism
 * IUPAC Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013 (Link; chapter 101: Nomenclature of Natural Products)
 * IUPAC Nomenclature of Steroids, Recommendations 1989 (Link; please note: Rules for hopanoids may differ from rules for steroids)
 * IUPAC Revised Section F: Natural Products and Related Compounds, 1999 (Link)
 * Review on biohopanoids
 * Review on geohopanoids