Arborane is a class of pentacyclic

triterpene Triterpenes are a class of chemical compounds composed of three terpene units with the molecular formula C30H48; they may also be thought of as consisting of six isoprene units. Animals, plants and fungi all produce triterpenes, including squal ...

consisting of organic compounds with four 6-membered rings and one 5-membered ring. Arboranes are thought to be derived from arborinols, a class of natural cyclic triterpenoids typically produced by

flowering plant Flowering plants are plants that bear flowers and fruits, and form the clade Angiospermae (), commonly called angiosperms. They include all forbs (flowering plants without a woody stem), grasses and grass-like plants, a vast majority of ...

s. Thus arboranes are used as a biomarker for

angiosperms Flowering plants are plants that bear flowers and fruits, and form the clade Angiospermae (), commonly called angiosperms. They include all forbs (flowering plants without a woody stem), grasses and grass-like plants, a vast majority of br ...

and

cordaites ''Cordaites'' is an important genus of extinct gymnosperms which grew on wet ground similar to the Everglades in Florida. Brackish water mussels and crustacea are found frequently between the roots of these trees. The fossils are found in rock s ...

. Arborane is a

stereoisomer In stereochemistry, stereoisomerism, or spatial isomerism, is a form of isomerism in which molecules have the same molecular formula and sequence of bonded atoms (constitution), but differ in the three-dimensional orientations of their atoms i ...

of a compound called fernane, the diagenetic product of fernene and fernenol. Because aborinol and fernenol have different biological sources, the ratio of arborane/fernane in a sample can be used to reconstruct a record for the relative abundances of different plants.

Background

Arborane, the

diagenetic Diagenesis () is the process that describes physical and chemical changes in sediments first caused by water-rock interactions, microbial activity, and compaction after their deposition. Increased pressure and temperature only start to play a ...

product of arborinol and isoarborinol, is a pentacyclic triterpene. Isoarborinol was first isolated from the Messel oil shale in 1969 by Albrecht and Ourisson. The discovery of isoarborinol derivatives in

sedimentary rock Sedimentary rocks are types of rock that are formed by the accumulation or deposition of mineral or organic particles at Earth's surface, followed by cementation. Sedimentation is the collective name for processes that cause these particle ...

s that predate the first angiosperms, particularly

Permian The Permian ( ) is a geologic period and stratigraphic system which spans 47 million years from the end of the Carboniferous Period million years ago (Mya), to the beginning of the Triassic Period 251.9 Mya. It is the last period of the Pale ...

and

Triassic The Triassic ( ) is a geologic period and system which spans 50.6 million years from the end of the Permian Period 251.902 million years ago (Mya), to the beginning of the Jurassic Period 201.36 Mya. The Triassic is the first and shortest period ...

s, contradicted previous knowledge that plants were the only biological source for arborinols. This discovery suggested that a non-plant source for arborinols existed during this period. The explanation behind the appearance of a plant-derived compound in the Permian and Triassic rock record remained unknown for nearly twenty years. Understanding the biological synthesis pathways for arborinols requires a combination of molecular biology and lipid analysis of the diagenetic products in sediments.

Biological Production

Oxadosqualene cyclase (OSC) is an enzyme typically found in plants that is used to synthesize arborinol and isoarborinol. OSC allows for

carbocation A carbocation is an ion with a positively charged carbon atom. Among the simplest examples are the methenium , methanium and vinyl cations. Occasionally, carbocations that bear more than one positively charged carbon atom are also encoun ...

intermediates that are necessary in the

cyclization A cyclic compound (or ring compound) is a term for a compound in the field of chemistry in which one or more series of atoms in the compound is connected to form a ring. Rings may vary in size from three to many atoms, and include examples where ...

of a 30-carbon acyclic

isoprenoid The terpenoids, also known as isoprenoids, are a class of naturally occurring organic chemicals derived from the 5-carbon compound isoprene and its derivatives called terpenes, diterpenes, etc. While sometimes used interchangeably with "terpenes" ...

which leads to the production of isoarborinol. OSC can produce both pentacyclic and tetracyclic organic compounds in plants, but was previously known to only produce tetracyclic compounds in

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

. ''

Eudoraea adriatica ''Eudoraea adriatica'' is a Gram-negative, aerobic and non-motile bacterium from the genus of ''Eudoraea ''Eudoraea'' is a genus of bacteria from the family of Flavobacteriaceae The family Flavobacteriaceae is composed of environmental b ...

'' is the first bacterium known to synthesize arborinols. E. adriatica, which was extracted from surface waters in the

Adriatic Sea The Adriatic Sea () is a body of water separating the Italian Peninsula from the Balkans, Balkan Peninsula. The Adriatic is the northernmost arm of the Mediterranean Sea, extending from the Strait of Otranto (where it connects to the Ionian Sea) ...

, is the only known bacterium to produce these pentacyclic triterpenes. The evolutionary pathway for OSC in bacteria is still unknown; however, E. adriatic is distinct from the isoarborinol synthase used in plants. This phylogenetic difference suggests that arboranes have been produced through multiple pathways in the OSC family.

Measurement

The structure of isoarborinol was first elucidated using

x-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angle ...

. More recently,

mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a '' mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is u ...

and

NMR spectroscopy Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fiel ...

are used to detect arborane and its derivatives. Arborane, along with other C-5 unsaturated compounds, has a base peak at m/z 274 and a strong peak at m/z 259. C-5 unsaturated compounds with an

isopropyl group In organic chemistry, propyl is a three-carbon alkyl substituent with chemical formula for the linear form. This substituent form is obtained by removing one hydrogen atom attached to the terminal carbon of propane. A propyl substituent is often ...

, which include both arborane and fernane, have an additional strong peak at m/z 231 that distinguish it from other C-5 unsaturated compounds. Arborane and fernane have nearly identical fragmentation patterns with slightly different abundances for certain peaks making them difficult to distinguish. One common method for differentiating the two stereoisomers is by using

gas chromatography Gas chromatography (GC) is a common type of chromatography used in analytical chemistry for separating and analyzing compounds that can be vaporized without decomposition. Typical uses of GC include testing the purity of a particular substance, ...

-isotopic ratio-mass spectrometry. Another common method is measuring the

optical rotation Optical rotation, also known as polarization rotation or circular birefringence, is the rotation of the orientation of the plane of polarization about the optical axis of linearly polarized light as it travels through certain materials. Circular ...

values.

Preservation

Arborinol is quite recalcitrant in

sediment Sediment is a naturally occurring material that is broken down by processes of weathering and erosion, and is subsequently transported by the action of wind, water, or ice or by the force of gravity acting on the particles. For example, sa ...

and has been detected in samples up to 50 million years old. When buried in sediment for time periods greater than 50 million years, both arborinol and isoarborinol can lose the

hydroxyl In chemistry, a hydroxy or hydroxyl group is a functional group with the chemical formula and composed of one oxygen atom covalently bonded to one hydrogen atom. In organic chemistry, alcohols and carboxylic acids contain one or more hydrox ...

functional group and convert to arborane under low temperatures via a process called

diagenesis Diagenesis () is the process that describes physical and chemical changes in sediments first caused by water-rock interactions, microbial activity, and compaction after their deposition. Increased pressure and temperature only start to play ...

. Under harsher conditions such as high temperatures, high acidity, or highly oxidizing environments, arborane can further breakdown into a wide variety of products including MATH (5-methyl-10(4-methylpentyl) des-A-25-norarbora(ferna)-5,7,9-triene), MAPH (25-norarbora(ferna)-5,7,9-triene), DAPH 1 (24,25-dinorarbora (ferna)-1,3,5,7,9-pentaene) and DAPH 2 (iso-25-norarbora (ferna)-1,3,5,7,9-pentaene). Because arborinol is almost exclusively produced by flowering plants, arborane and its derivatives are used as a

biomarker In biomedical contexts, a biomarker, or biological marker, is a measurable indicator of some biological state or condition. Biomarkers are often measured and evaluated using blood, urine, or soft tissues to examine normal biological processes, p ...

for

angiosperm Flowering plants are plants that bear flowers and fruits, and form the clade Angiospermae (), commonly called angiosperms. They include all forbs (flowering plants without a woody stem), grasses and grass-like plants, a vast majority of br ...

s. These

molecular fossil A biosignature (sometimes called chemical fossil or molecular fossil) is any substance – such as an element, isotope, or molecule – or phenomenon that provides scientific evidence of past or present life. Measurable attribute ...

s can provide information on the geographic distribution of plants in early Earth.

Case Study: Saar-Nahe Basin

The hydrocarbon composition of thirty-seven samples of coal extracted from boreholes in the Saar-Nahe Basin in southwestern

Germany Germany, officially the Federal Republic of Germany (FRG),, is a country in Central Europe. It is the most populous member state of the European Union. Germany lies between the Baltic and North Sea to the north and the Alps to the sou ...

were analyzed in a 1994 study. The samples are from the Upper Carboniferous (360 to 299 Mya) or Lower

(299 to 251 Mya) periods. Mass spectrometry and NMR were used to identify 5-methyl-10-(4-methylpentyl)-des-A-25-norarbora(ferna)-5,7,9-triene (MATH) and 25-norarbora(ferna)-5,7,9-triene as the two most abundant compounds. These two hydrocarbons are derivatives from isoarborinol and fernenes that are thought to form from a 4,5-cleavage following a methyl-shift in an arborane/fernane precursor under strongly acidic conditions. The results from this study suggest that the arborane/fernane precursors may have been produced by higher plants such as ''Pteridospermales'' and Coniferophytes.

Case Study: European Carboniferous and Permian Coals

A 2012 study aimed to connect

climate Climate is the long-term weather pattern in an area, typically averaged over 30 years. More rigorously, it is the mean and variability of meteorological variables over a time spanning from months to millions of years. Some of the meteorologica ...

patterns to the organic matter compositions of various

coal Coal is a combustible black or brownish-black sedimentary rock, formed as stratum, rock strata called coal seams. Coal is mostly carbon with variable amounts of other Chemical element, elements, chiefly hydrogen, sulfur, oxygen, and nitrogen ...

and lacustrine samples throughout Europe from the Carboniferous and Permian periods. Both arboranes and fernanes were found in samples from the Donets Basin (

Kasimovian The Kasimovian is a geochronologic age or chronostratigraphic stage in the ICS geologic timescale. It is the third stage in the Pennsylvanian (late Carboniferous), lasting from to Ma.; 2004: ''A Geologic Time Scale 2004'', Cambridge Universi ...

), the Saar Basin (Early Stephanian), the Puertollano Basin (Late Stephanian), the Autun Basin (Autunian) and the Buxieres Basin (Autunian). Neither were detected in the Visean samples from the

Moscow Basin The Moscow Basin is a major sedimentary basin and tectonic structural feature in the stable East European Craton. It has been widely studied by Russian and Scandinavian geologists. Formation and geological history The Fennoscandia Shield and its ...

or the

Moscovian Moscovian may refer to: *An inhabitant of Moscow, the capital of Russia *Something of, from, or related to Moscow *Moscovian (Carboniferous) The Moscovian is in the ICS geologic timescale a stage or age in the Pennsylvanian, the youngest subs ...

samples from the Donets and Saar Basins. The arborane/fernane ratio is an indication of

and possibly

seed ferns A seed is an embryonic plant enclosed in a protective outer covering, along with a food reserve. The formation of the seed is a part of the process of reproduction in seed plants, the spermatophytes, including the gymnosperm and angiosperm p ...

; therefore, the maximum in this ratio is associated with the presence of cordaites and possibly

gymnosperm The gymnosperms ( lit. revealed seeds) are a group of seed-producing plants that includes conifers, cycads, '' Ginkgo'', and gnetophytes, forming the clade Gymnospermae. The term ''gymnosperm'' comes from the composite word in el, γυμν ...

s. The abundances of other

aromatic In chemistry, aromaticity is a chemical property of cyclic (ring-shaped), ''typically'' planar (flat) molecular structures with pi bonds in resonance (those containing delocalized electrons) that gives increased stability compared to sat ...

and

aliphatic In organic chemistry, hydrocarbons ( compounds composed solely of carbon and hydrogen) are divided into two classes: aromatic compounds and aliphatic compounds (; G. ''aleiphar'', fat, oil). Aliphatic compounds can be saturated, like hexane, ...

compounds from these samples along with arborane/fernane were used to propose a record for wet and dry cycles in Europe.

References

{{Reflist __FORCETOC__ Pentacyclic compounds Triterpenes Isopropenyl compounds