Intern:Quinones and related compounds with isoprenoid chain

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This guideline deals with the compound class of isoprenoid quinones and other electron-carrying isoprenoid lipids. These lipids consist of a polar carbocyclic head and an isoprenoid tail. They play an important role in many electron transfer processes like photosynthesis and the respiratory chain.

=Subclasses and definitions= The following subclasses of compounds can deal as electron carriers (all with added isoprenoid chain; IUPAC conform abbreviations in brackets, with n = number of isoprene subunits):
 * quinones

(aromatic compounds with an even number of keto-groups (C=O))
 * menaquinones (MK-n)
 * ubiquinones (Q-n)
 * plastoquinones (PQ-n)
 * phylloquinones (K)
 * tocoquinones (no abbr.)
 * x-tocopherolquinones (no abbr.)
 * x-tocotrienolquinones (x-T-3)
 * chromenols and chromanols

(chromene/benzopyrans and chromane/benzodihydropyran with one or more hydroxyl-groups; carrying an oxygen heteroatom)
 * menachromenols (MK-n-el)
 * ubichromenols (Q-n-el)
 * plastochromenols (PQ-n-el)
 * phyllochromenols(K-el)
 * tocochromenols (no abbr.)
 * phenazines

(compounds based on the phenazine-ringsystem; carrying two nitrogen heteroatoms)
 * metanophenazines (no official abbreviation)
 * x-tocopherols (x-T)
 * x-tocotrienols (x-T)

Definitions will follow.

Apart from tocopherols, no chromenols or chromanols and other tocol-compounds can be found in PANGAEA, yet. Therefore, this guideline will focus on quinones.

=Systematics and Nomenclatures=

IUPAC nomenclature
The official nomenclature of the International Union of Pure and Applied Chemistry (IUPAC) for all substances listed above can be found here:
 * IUPAC (1973): Nomenclature of Quinones with Isoprenoid Side-Chains (PDF)

For tocopherols and related substances, a more detailed nomenclature can be found here:
 * IUPAC (1983): Nomenclature of Tocopherols and Related Compounds (PDF)

The nomenclature mainly deals with proper trivial names and abbreviations. However, the common IUPAC rules for systematic names apply (according to IUPAC Nomenclature of Organic Chemistry 2013).

Semisystematic names
Because the systematic IUPAC names for quinones can be very long, semisystematic names can be a solution to shorten the names. Retained names for side chain building blocks can be used for this purpose.

List of building blocks:
 * prenyl (= 3-methyl-2-butenyl )
 * phytyl (= (E)-(7R,11R)-3,7,11,15-tetramethyl-2-hexadecenyl)
 * farnesyl
 * geranyl

Notation for unsaturation of isoprenoid chain
The notation used for displaying the unsaturation status of an isoprenoid chain is an addition to the IUPAC recommendations of abbreviations. This notation is rather rarely used and is no official nomenclature. Therefore, it can be used in slightly differing ways by different sources. This notation is especially used for biomarker analyses of isoprenoid electron carrier compounds.

Numbering system: Number of isoprene-units vs. number of carbons
While IUPAC recommends the usage of "n = number of isoprene units in side chain", some ressources still use the old nomenclature with "n = number of carbon atoms in isoprenoid side chain".

This discrepancies can be especially confusing for trivial names. The IUPAC notation should always be prefered for parameter names, however, terms according to the old nomenclature can be given as synonyms within the terminology catalogue.

The conversion of trivial names using different numeration systems is defined by the amount of carbon atoms per isoprene unit (5 carbons):

n (IUPAC) = number of isoprene units = number of carbons / 5

n (old) = number of isoprene units * 5 = number of carbons

Example:

ubiquinone-10 (preferred) = ubiquinone 50

Please note:

Vitamin notations always use the number of carbons.

Abbreviations and cofactor notations always use the number of isoprenes

=Hydrogenation of quinones and related substances=