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= Follows. Hopanoid lipids play a similar role in prokaryots, as sterol lipids (e.g. cholesterol) do in eukaryots.

The differences and similarities between hopanoids and sterol lipids are listed in the following table:

Homohopanoids
=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).

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 to avoid ambiguity. The recommended full descriptions are listed in this table:

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

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

However for polycyclic compounds like hopanoids, (...)

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 "dinor-", "trinor-" etc. are used.

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 (1089), 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 17alpha-21beta trishomohopane" can be shortened to "22S 17alpha-21beta trishomohopane"

Chirality of homohopanoids
The C22-position of the hopanoid base structure is prochiral (see prochirality in IUPAC gold book).

=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