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Appendix 1 Glossary of Chemical Terms

This appendix comprises a glossary of selected chemical terms used in this volume. Many of the definitions included in this glossary were derived from the following sources: (1) Tissot and Welte (1979), Formation and Occurrence; (2) Daintith (1990), A Concise Dictionary of Chem- istry; (3) Miles (1989), Illustrated Glossary ofPetroleum Geochemistry; and (4) the glossary in Hunt (1996), Petroleum Geochemistry and Geology. Additional definitions can be found in these refer- ences as well as the chapters of this volume.

acyclic compounds: Organic molecules with a chain or and oxygen. They are usually soluble in disul- branched structure and no cyclic subunits. · fide. Asphalts contain heavy oils, resins, asphaltenes, addition: A type of polymerization in which many mole- and high-molecular-weight waxes. cules of a monomer are simply added together. asphaltenes: Asphaltic constituents of crude oil that are sol- alcohols: Alcohols are aliphatic compounds with the gen- uble in carbon disulfide but insoluble in petroleum eral formula ROH, where R is any or substituted ether or n-. Asphaltenes are agglomerations of alkyl group and OH is an hydroxyl group. molecules with condensed aromatic and naphthenic alginite: See liptinite (see Table 1 in Leventhal and Gior- rings connected by paraffin chains. They have molecular dano, 2000). weights in the thousands. aliphatic compounds: See saturated compounds. asphaltite: Black to dark brown, comparatively hard, solid : containing no double or triple bitumens that soften at temperatures above 100°C and bonds, composed only of and carbon, and are usually soluble in carbon disulfide. Examples are usually having the formula CnH2n+ 2 (for acyclic struc- gilsonite, glance pitch, and grahamite. tures) or CnH2n (for cyclic structures). biomarker (geochemical fossil or molecular marker): Or- alkyl group: Saturated hydrocarbon group with one less hy- ganic compound whose carbon structure, or skeleton, is drogen than the parent alkane and having the general formed by living organisms and is sufficiently stable to formula CnH2n+l; sometimes denoted by the symbol R be recognized in crude oil or in the organic matter of (e.g., -CH3, methyl group; -C2H 5, ethyl group; etc.). ancient sediments. Typical biomarkers are the por- amphipathic: A term used to define a molecule with a phyrins, pristane, phytane, steranes, carotanes, and pen- polar head and a nonpolar tail. tacyclic triterpanes. API gravity: The density of oil measured with a hydrometer biopolymer: Polymer synthesized in a living organism. having a scale developed by the American Petroleum In- bitumen: Sedimentary liquid or solid substances of variable stitute and given in units of oAPI (degrees API): oo API color, hardness, and volatility, composed principally of gravity= 1.076 g/cm3, 20° API gravity= 0.9340 g/cm3, the elements carbon and hydrogen and soluble in or- 50° API gravity= 0.7796 g/cm3. oAPI is related to the ganic solvents and carbon disulfide. It is derived from density or specific gravity (S.G.) of oil at 60°F by the fol- during catagenesis and includes crude oil. lowing formula: oAPI = (141.5/S.G. at 60°F)-131.5. branched-alkane: An acyclic alkaQe molecule that has one arenes: that contain both aliphatic and aro- or more alkyl groups bonded to a hydrocarbon chain matic units. with three or more other carbon atoms (e.g., iso- aromatic compounds: A general term for compounds con- prenoids). taining one or more or substituted benzene BSR: Bacterial sulfate reduction. Bacteria use sulfate and rings and compounds that resemble benzene in chemi- organic matter to form and carbon cal behavior (see Part 5 in Appendix 2 of this volume). dioxide. aromatic hydrocarbons: Cyclic or polycyclic aromatic com- carbonaceous: Organic-rich, or containing organic matter. pounds consisting of only carbon and hydrogen. Exam- carboxylic acid: A class of compounds which contain the ples include benzene, , etc. (see Part 5 in carboxyl group (-COOH) attached to aliphatic (alkyl) Appendix 2 of this volume). or aromatic (aryl) hydrocarbon groups (see Part 1 in aryl group: The aryl group signified by the symbol Ar com- Appendix 2 of this volume). prises the aromatic compounds phenyl and substituted catagenesis: The principal hydrocarbon generation stage of phenyls as well as polynuclear aromatic compounds. organic matter maturation in sedimentary basins and cor- asphalt: Black to dark brown solid or semisolid bitumens responding to temperatures between 50° and 150oC and that gradually liquefy when heated. They are composed pressures from 300 to 1,500 bars. Kerogen evolves during principally of the elements carbon and hydrogen but this stage to produce the first liquid petroleum. Both liq- also contain appreciable quantities of nitrogen, sulfur, uid oil and condensates are accompanied by significant

315

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amounts of . The end of catagenesis is reached in hard base: An electron donor atom of low polarizability the range where the disappearance of aliphatic carbon and high electronegativity. Hard bases are usually small chains in kerogen is complete. The equivalent vitrinite re- and highly charged and tend to bond ionically. flectance range would be 0.5 to 2.0 percent. HC: Refers to (1) Hydrogen, carbon or (2) hydrocarbon. CHO: Carbon, hydrogen, oxygen. heteroatoms: Atoms in organic compounds other than car- complex ion: See metal complex. bon and hydrogen; for example, nitrogen, oxygen, and condensation: A type of polymerization in which monomer sulfur. molecules combine by the loss of some simple mole- heterocompounds: Organic compounds that contain a het- cules, usually water. eroatom such as nitrogen, oxygen, or sulfur. CPI: Carbon preference index. The ratio of odd to even heterocyclic compounds: Cyclic compounds in which one normal in a specific molecular weight range or more of the carbon atoms in the ring is replaced by (usually c25 to c34) . an atom of another element such as nitrogen, oxygen, CSIA: Compound specific isotope analysis. or sulfur. cyclic compounds: Organic compounds with ring structures. HI: See hydrogen index. dalton: Measure of atomic mass of molecules in terms of : Compounds (homologs) having similar atomic mass units (i.e., molecular weight). structure but differing in the addition or subtraction of dealkylation: The loss of an alkyl group from an organic aCH2 group. compound. HPLC: High-performance liquid chromatography. decarboxylation: The loss of a carboxyl group from an or- HRMS: High-resolution mass spectrometry. ganic compound, for example, the conversion of alkyl humic acid: See humic substances. acids to alkanes. humic (type) organic matter: A general term, not to be con- dehydration: The loss of H20 from an organic compound. fused with humic substances or materials. It is the decom- DOC: Dissolved organic carbon. position and polymerization product of the lignin, tan- DOP: Degree of pyritization (see Leventhal and Giordano, nins, and cellulose of plant-cell and -wall material, plus 2000). carbonized organic matter deposited in swamps and soils EPR: Electron paramagnetic resonance spectroscopy. under aerobic conditions with lower than normal oxygen equilibrium state: A state of thermodynamic equilibrium at- content. Kerogen types III and N are humic in nature. tained for a system or chemical species if its properties humic substances (humic material): Humic substances are do not change with time and if it returns to that state geopolymers formed in soil and sediment. They are after having one or more of its properties slightly amorphous, brown or black colored, acidic, and poly- changed and then change back spontaneously. disperse (i.e., consisting of a number of ill-defined com- ESR: Electron spin resonance spectroscopy. pounds), with molecular weights in the range of several EXAFS: Extended X-ray absorption fine structure. hundreds to tens of thousands. Humic substances gen- extract: Oil or oil-like products which are removed from erally contain subequal portions of C, H, and 0. They rock samples by using organic solvents. are generally divided into three fractions: ( 1) humic fatty acids: Aliphatic carboxylic acids (alkanoic acid). acid (HA), which is soluble in dilute alkaline solutions free radical: An atom or molecule possessing an odd ( un- but precipitates upon acidification; (2) fulvic acid (FA), paired) electron. which is soluble in alkaline solutions and remains solu- fulvic acid: See humic substances. ble in acid; and (3) humin, which is insoluble in acid functional group: Group of two or more atoms that has a and base. Typically, fulvic acids have molecular weights specific structure and characteristic chemical proper- less than 5,000 while humic acids have molecular ties, e.g., hydroxyl, -OH-; carboxyl, -COOH; amino, weights greater thari 5,000. -NHx; methyl, -CH3; sulfhydryl, -SH. humin: See humic substances. GC: Gas chromatography. hump: See UCM. GC-MS: Gas chromatography-mass spectrometry. hydrocarbon: A compound composed of only the elements geochemical fossil: See biomarker. hydrogen and carbon. Bituminous material such as pe- geopolymer: Polymer or macromolecule synthesized in soil troleum is composed principally, but not exclusively, of and sediments (e.g., humic substances). hydrocarbons. graphitization: Conversion of organic matter to graphite by hydrogen index (HI): HI = mg of generated hydrocar- the elimination ofO, H, N, and other atoms and the or- bons/gram of organic carbon, as determined from the s2 dering of the remaining carbon into the crystal structure peak during Rock-Eval pyrolysis (see Rock-E val pyrolysis). of graphite. ICP-MS: Inductively coupled-plasma mass spectrometry graphitizing carbon: Carbon that, upon heating, produces inertinite: A maceral group that shows little or no reaction true graphite. during heating and is derived from oxidation processes. hard acid: An electron acceptor atom characterized by a Inertinite includes fusinite (fossil charcoal), scleroti- small size, high positive oxidation state, and absence of nite, derived from fungal remains, and other high- any outer electrons which are easily excited to higher carbon material with low hydrogen content and high re- states. Hard acids tend to bond ionically. flectance. It shows no fluorescence behavior.

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isomers: Compounds with the same empirical formula but They are discrete particles characterized by size, chemi- different three-dimensional structures; that is, mole- cal, physical, and optical properties, which require mi- cules with the same number and kinds of atoms but rep- croscopy for identification. resenting diflerent substructures. When two different macromolecule: A high molecular mass (>1,000 dalton) arrangements in three dimensions of a molecule are molecule. possible by bond rotation, then the isomers are referred mercaptans: See thiols. to as stereoisomers or conformational isomers (con- mesophase: Organic substances with a structural state in- formers). Stereoisomers differ in the spatial arrange- termediate between the ordered crystalline state and the ment of groups, for example, cis- and trans- (boat and isotropic liquid state; sometimes referred to as a liquid chair) structures. Structural (or configurational) iso- crystal or paracrystal. mers differ in the way that the atoms are linked together, metagenesis: Stage of organic matter maturation in sedi- for example, n- and . Optical isomers mentary basins corresponding to temperatures between are nonidentical mirror images comparable to right 150° and 250°C. During metagenesis, organic matter is and left handed gloves (see Simoneit and Gize, 2000). composed primarily of methane and a carbon residue in isoprenoid: A hydrocarbon with a molecular structure con- which some crystalline ordering begins to develop. It is taining the basic unit isoprene, consisting of five carbon equivalent to a range of between 2 and 4 percent vitri- atoms, with a branch at the second atom, as shown below: nite reflectance. metastable: See metastable equilibrium. c metastable equilibrium: A system or species is in a state of I metastable equilibrium and is said to be metastable if it C=C-C=C remains in a state of equilibrium while its chemical con- This is the basic building block of many natural products figuration (mol~cular arrangement or structure) does such as terpenoids, steroids, , pristane, and not correspond to the lowest possible energy level. phytane. Many petroleum hydrocarbons are diagenetic metal complex: Metal complexes are structures containing derivatives of isoprenoid polymers. The designations ip- a central metal cation bonded to surrounding species 18, ip-19, and ip-20 refer to isoprenoids with 18, 19, and called ligands. 20 carbon atoms, the latter two being pristane and phy- metal-organic complex: Metal-organic complexes are struc- tane, respectively. tures in which a metal cation is attached to one or more IUPAC: International Union of Pure and Applied Chemistry. organic ligands by direct bonding to electron-donor kerogen: Sedimentary organic matter that is insoluble in atoms other that carbon, most commonly oxygen, sulfur, nonoxidizing acids, bases, and organic solvents. It is a and nitrogen. complex mixture of high-molecular-weight organic com- micelle: A spherule of amphipathic molecules in water, pounds. Humic substances evolve to form kerogen and with the polar heads forming the surface and the non- kerogen evolves to produce bitumen. polar tails pointing toward the interior. LC: Liquid chromatography. molecular marker: See biomarker. Lewis acid: Any species that is capable of accepting a pair of monomer: Simple compounds from which polymers are electrons. made. Lewis base: Any species that is capable of donating a pair of MS: Mass spectrometry. electrons. NAA: Neutron-activation analysis. LFER: Linear free energy relationship. n-alkane: A straight-chain alkane containing no branches ligand: A chemical species that is bonded to a central metal and having the general formula CnH2n+2; for example, cation in a metal complex and is characterized as an methane, , , n-butane, and n-pentane. electron donor atom or a compound that contains one naphthene: Cycloalkane hydrocarbons with a formula or more electron donor atoms. CnH2n• lignin: A group of wood constituents comprising high-mol- nongraphitizing carbon: Carbon that, upon hearing, pro- ecular-weight polymers based on units constructed from duces graphite-like layers that are in parallel groups but phenyl-propane derivatives. are not orientated as in true crystalline graphite. lipids: A broad term applied to organism-produced sub- nonpolar compounds: Compounds in which the center of stances that are oil soluble and water insoluble such as negative charge is the same as the center of positive fats, waxes, fatty acids, sterols, pigments, and terpenoids. charge and, hence, all external regions of the molecular liptinite: A maceral group that includes sporinite, cutinite, structure are electrically neutral. resinite, and alginite, which are derived from spores and NSO: Nitrogen, sulfur, and oxygen; also the name given to the pollen, cuticle, resins, and algae, respectively. nonhydrocarbon portion of petroleum and rock extracts. maceral (coal mineral): Microscopically recognizable con- 01: See oxygen index. stituents of solid organic matter in rocks that can be dif- oil window: Time and temperature conditions that lead to ferentiated by their morphology. Macerals are analogous the formation of oil from kerogen in sediments; in to minerals of inorganic rocks but differ in having less terms of temperature, generally benveen 50° and l50oc uniform chemical composition and physical properties. over millions of years.

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organic componnds: Compounds containing carbon-to- consist of polypeptides, which are long chains (poly- carbon (C-C) and/ or carbon-to-hydrogen ( G-H) bonds. mers) of amino acids, and form enzymes and other di- organic matter: A broad term that includes all carbon-rich verse components of organic matter. Proteins are insol- materials (usually of biological origin) containing or- uble in water but decompose readily to amino acids in ganic compounds or derived from compounds contain- the water column and surface sediments. ing carbon and hydrogen. pyrobitumen: Black to dark brown, hard bitumens that are organometallic componnds: Organometallic compounds infusible and relatively insoluble in carbon disulfide and are species in which a central metal atom is bonded cova- other organic sovents. Albertite and impsonite are pyro- lently to at least one carbon atom of a surrounding or- bitumens. Pyrobitumen may be difficult to distinguish ganic molecule (e.g., tetraethyllead and methyl mercury). from kerogen and represents either a residue remaining oxygen index (OI): 01 == mg of generated C02 per gram of in source rocks after oil generation or migrated, heated, organic carbon as determined from Rock-Eval pyrolysis and solidified crude oil in nonsource rocks. (see Rock-Eval pyrolysis.) pyrolysate: Product of pyrolysis. PAH: Polycyclic aromatic (polynuclear) hydrocarbons; for pyrolysis: Nonoxidative heating of organic matter that results example, naphthalene. in bond breaking and the production oflower molecular- parafrm: See alkane. weight organic fractions. This process involves the heating petroleum (literally, rock oil): Natural gas and liquid bitu- of carbonaceous rocks or organic matter in the laboratory men (crude oil); both are composed principally of hy- to generate hydrocarbons by thermal decomposition. drocarbons. Some definitions do not include natural gas. Heating in the presence of water is called hydrous pyroly- phenols: Phenols are compounds of the general formula sis, and heating in the absence of water is called anhydrous ArOH, where Ar is any aryl or substituted aryl group; pyrolysis (see Rock-Eval in this glossary.) sometimes referred to as aromatic alcohols (see Part 3 in reflectance: Reflection of light from a polished surface. Re- Appendix 2 of this volume.) flectance of organic constituents in a polished section is phenolic group: Hydroxyl group (-OH) attached to a ben- reported as R,%, signifying a measurement of percent zene ring or other aryl group. reflectance using oil immersion at a wavelength of 546 ± phenyl group: The benzene ring less one hydrogen, -C6H5. 10 urn (see Gize, 2000). phytane: A saturated branched hydrocarbon chain (iso- resinite: Maceral in the liptinite group. Resinites are fossil- prenoid) with 20 carbon atoms. free resins derived from balsam, mastic, latex, and some polar componnds: Organic compounds with external, mol- plant gums, waxes, oils, and fats. Amber and copal are ecular regions of partial positive and partial negative resinites. charges. All nitrogen, sulfur, and oxygen compounds Rock-Eval (pyrolysis): A temperature-programmed pyroly- and aromatic compounds are polar. sis (anhydrous) of organic matter to show petroleum po- polycyclic componnds: Organic molecules composed of tential or for characterization. Heating is conducted at two or more rings joined together (fused) by shared car- 20°C/minute from 250° to 590°C. The first fraction is bon atoms. volatile hydrocarbons (S1 peak); the second fraction is polymer: A compound composed of a very large molecule pyrolyzable hydrocarbons released between 350° and or molecules formed by the joining together of smaller 480°C (S2 peak); and the third is an S3 peak produced identical molecules (monomers). from pyrolyzable C02 released between 250° and 390°C. polymerization: The joining together of many small mole- sapropelic organic matter: The decomposed and poly- cules of the same type (monomers) to make a very large merization products of high-lipid organic materials, molecule. such as spores and planktonic algae deposited in sub- polynuclear (aromatic) componnds: Aromatic polycyclic aqueous muds (marine or lacustrine) under predomi- compounds. nantly anaerobic conditions. Kerogen types I and II are potphyrins: Derivatives of the in plants and the sapropelic. in blood. have a basic structure saturated : Two or more carbons linked by sp3 hy- consisting of four interconnected rings, each ring con- bridized bonds; frequently termed single bonds. taining four carbon atoms and one nitrogen atom saturated componnds: General term that includes normal ( structure), plus various other side chains of and branched alkanes and cycloalkanes as well as other carbon. In living organisms, hemoglobin is complexed compounds. They are saturated with hydrogen; that is, with iron and chlorophyll is complexed with magne- they have no double or triple bonds between carbon sium. The porphyrins in kerogen and bitumen are atoms. Saturated compounds are referred to as aliphatic sometimes complexed with V, Ni, Fe, Cu, and Mn. compounds. pristane: A long-chain, branched, saturated isoprenoid saturated hydrocarbons: Compounds consisting of only containing 19 carbon atoms. carbon and hydrogen, and containing the maximum pristane/phytane ratio: The ratio of the relative abun- number of hydrogen atoms possible, i.e., lacking G-C dance of pristane and phytane. double or triple bonds (see saturated compounds and proteins: Proteins form the bulk of lower plants and ani- saturated carbons). mals and are minor components of higher plants. They SHRIMP: Sensitive high-resolution ion microprobe.

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soft acid: An electron acceptor atom with one or more of unsaturated carbons: Carbon atoms linked by sp2 hy- the following properties: low positive or zero charge, bridized bonds; frequently termed double bonds. large size, and several easily excited outer electrons. unsaturated compounds: Compounds that have double Tends to bond covalently. and triple bonds between carbon atoms, which means soft base: An electron donor atom of high polarizability and that they are unsaturated with respect to hydrogen. Aro- of low electronegativity that is easily oxidized or is asso- matics, olefins, resins, and asphaltenes are unsaturated ciated with empty, low-energy orbitals. It is usually large compounds in petroleum, consisting of branched and with low or zero charge and tends to bond covalently. cyclic compounds. stable: See stable equilibrium. UCM: Unresolved complex mixture. Sometimes referred stable equilibrium: A system or species is in a state of stable to as the hump in a gas chromatogram. equilibrium and is said to be stable if, under a given set vitrinite: A maceral group consisting of components de- of conditions, it has the one chemical configuration rived from woody, terrestrial plant sources. It not only (molecular arrangement) that corresponds to the lowest shows a progressive increase in reflectance with thermal energy level. maturation but it is relatively common and homoge- steranes: The alkanes derived from steroid natural prod- neous in its chemical and physical properties. Conse- ucts. They are found in oil and source-rock extracts, but quently, vitrinite reflectance provides the standard ther- are not found in living organic matter. mal maturity index in organic studies. steroids: A group comprising cyclic isoprenoid compounds vitrinite reflectance: A maturation parameter based on the containing six isoprene units but fewer methyl groups change in reflectance of polished vitrinite particles with than related triterpenoids. They are synthesized in increasing time and temperature. Common abbrevia-

, , plants and animals but are rare in bacteria and blue- tions for vitrinite reflectance are VR0 R0 ~. ~ax• green algae. ~in• ~ean• and %Ro. sterols: Members of the steroid group containing a hy- water washing: A process whereby formation water, or droxyl (OH) functional group. ground water, selectively removes the more soluble com- terpenoid: An isoprenoid polymer usually containing 10, ponents of oil, i.e., lighter hydrocarbons and aromatic 15, 20, 30, or 40 carbon atoms (mono-, sesqui-, di-, tri-, compounds, thus causing a lower API gravity. and tetra-, respectively). Terpenoids include hydrocar- wax: Part of the lipid fraction of organic matter. Waxes are bons, alcohols, and acids. Among the common ter- usually from the protective coating of leaves and are panes (hydrocarbon terpenoids) are the hopanes. composed of long-chain normal alkanes and alcohols tetrapyrrole: A group of compounds, including porphyrins, with chain lengths from C16 to C36. In sediments, alco- that contain four units. Pyrrole is an aromatic hols undergo alteration to normal alkanes. The term is five-member cyclic molecule containing four carbons used informally to describe bituminous material that is and one nitrogen in the ring. solid at room temperature, has a characteristic luster thermal stability: The capacity of a species with a given and oily feel, and principally is composed of saturated chemical configuration to remain stable or metastable at hydrocarbons that are soluble in carbon disulfide. a given temperature. XANES: X-ray absorption near-edge-structure spectroscopy. THC: Total hydrocarbon. thiols: Organic compounds that contain at least one REFERENCES sulfhydryl (-SH) functional group. They are also re- Giie, A.P., 2000, Organic petrology applied to ore deposits: Reviews in ferred to as mercaptans. Economic Geology, v. 9, p. 63-86. TLC: Thin-layer chromatography. Leventhal,J.S., and Giordano, T.H., 2000, The nature and roles of organic matter associated with ores and ore-forming systems: An introduction: T max: The temperature at which the maximum yields of S 2 Reviews in Economic Geology, v. 9, p. 1-26. peak hydrocarbons are produced during Rock-Eval py- Simoneit, B.R.T., and Gize, A.P., 2000, Analytical techniques for organic rolysis (see Simoneit and Gize, 2000). matter characterization in ore deposits: Reviews in Economic Geology, TOC: Total organic carbon. v. 9, p. 27-62. TSR: Thermochemical sulfate reduction. Sulfate and or- ganic matter react at temperatures above about 150oC to yield hydrogen sulfide and carbon dioxide.

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This appendix comprises a glossary of selected organic compounds mentioned in this volume. The common and IUPAC name, empirical formula, and structure are given for molecules in the following groups: (1) carboxylic adds, (2) amino acids, (3) phenols and alcohols, (4) carbohydrates, (5) aromatic compounds, (6) alkanes and , (7) biomarkers, (8) organosulfur and organonitrogen compounds, and (9) miscellaneous compounds. Complex organic material such as humic substances, kerogen, and bitumen are described in several chapters of this volume and are not included in this glossary.

Part I. Carboxylic acids Common Name IUPACName Molecular Formula Chemical Structure

Acetic Ethano1c acid

Butanoic acid 0 n-Butyric. ~OH

0 Caproic Hexanoic acid C6H1202 ~OH ~------Caprylic Octanoic acid CsHt602 ~OH

------~o:~oiliyd~iyph;;~~i------~------carreic propenoic acid C9H804 HOJQJ OH ~------Q~~i~2~!~~~~~~32~l------~------2-Hydroxy-1,2,3-propanetri- · l l l Citric carboxylic acid CoHs07 Hif ~-.....r 'OH 00 ------~(4-H;&;~ph~yD~:------~------p-coumaric propenoic acid C9Hs03 JQJ oo ------~~1~~~~PE~~:~2L------~------Heptanoic acid 0 Enanthic ~OH ------~~:H;&o;y:~------;------I Ferulic methoxyphenyl)-2-propenoic acid C10H1004 ~oo ~------~~~~~!~~~~~~o~~~~E~~~------Formic Methanoic acid CH202 i' ------a------H-co,H H_..,..__OH Fumaric (E)-Butenedioic acid C4H404 HO-{-(-OH ·~.~:------~~.::::~:::~------~~~~;:------~------

00 ~~------;:.~~~;d~:.~:,~:::;----~:~~~------=~------I ------OH \ 321

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Part 1. Carboxylic acids, continued Common Name IUPACName Molecular Formula Chemical Structure ------o------Glucuronic D-Glucuronic acid C6H 0 HOA.yoy"" 10 7 HO""Y·"'OH ------OH Glutaric Pentanedioic acid

Hydroxyethanoic acid Glycolic (hydroxyacetic acid)

~:~;drox benzoic 2-Hydroxybenzenecarboxylic acid C7H60 3 see salicylic -----~------p- or 4-Hydroxybenzenecarboxylic acid 4-Hydroxybenzoic HOffoo ------Lactic 2-Hydroxypropanoic acid ~00 ------~------Linoleic (Z,Z}-9, 12-0ctadecadienoic acid ~00

Maleic (Z}-Butenedioic acid ------0------Malic Hydroxybutanedioic acid C4H60 5 Ho.J..yyoo ------OH 0 Malonic Propanedioic acid

3-Mercapto------3-Mercaptopropanoic acid propionic ~~~;~::~:~;----~h~~~~f~~edTJc~T;-----~~~~------~~~------0------0 SH ~~~~~~::: ~~~~~~~~~~~:::~------~~H~~~------~~~------______0 Tetradecanoic acid Myristic ~OK ~;a~~------;~:n~~~~~~i------~~~~~------:~;------

------~------0 Palmitic Hexadecanoic acid ~OH

Palmitoleic (Z}-9-Hexadecenoic acid C 16H300 2 ~"" ------~------p-Phthalic 1,4-Benzenedicarboxylic acid C8H60 4 ~oo

0 Pimelic------Heptanedioic acid

Propionic Propanoic acid ~OH 0

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Part 1. Carboxylic acids, continued Common Name IUPACName Molecular Formula Chemical Structure ;;~~;------~~~~~~~~~;~~;------~~~~~------~~------

0 ;~~y~~------~~~~~~::~~------~~~~------~=------

Stearic------Octadecanoic acid 0 OH

0 Suberic Octanedioic acid C8H120 4 HO~OH

------~------0 Succinic Butanedioic acid C4H60 4 Ho~oH

r------,------o-.,..------·3-( 4-Hydroxy-3,5- o Sinapic (Synapic) dil;nethoxy~henyl)-2-propenoic c11 H12o5 cH,o~oH actd (3,5-dtmethoxy-4-hydroxy- Ho~

~------~~n~~:~~L------~~------0 Syringic 3,5-Dimethoxy-4-hydroxy- c H cH:P~OH 9 1005 benzoic acid HoA:f ------OCH, Tartaric 2,3-Dihydroxybutanedioic acid C4H60 6 Ho~oH OH 0

r------0 0 'T c4~04S I Thiodiacetic 2,2 Thiobisacetic acid HO~S~OHn

3,3'-Thiodipropionic 3,3'-Thiobispropanoic a~id Cc;H 0 S ~ 10 4 HO~S~OHi

------·0 ~~0 8 HS I Thioglycolic Mercaptoethanoic acid 2 ~OH ~------· Thiolactic 2-Mercaptopropanoic acid C3~02S ~OH SH ~------0------Thiosalicylic 2-Mercaptobenzoic acid C7H60zS cx::OH

------~------0 p-Toluic 4-Methylbenzoic acid C8H802 ffOH

~------Trimesic 1,3,5-Benzenetricarboxylic acid C9H606 HOWOHX .. 0 OH ~------iso-Valeric . 3-Methylbutanoic acid C H 0 I ~ 5 10 2 ~OH

r------0 n-Valeric Pentanoic acid ~OH ~------0 . • 4-Hydroxy-3-methoxybenzoic c H 0 cH,odOH Vant 11tc 'd s s 4 ~ ~

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Part 2. Amino acids Common Name IUPACName Molecular Formula Chemical Structure

Alanine Alanine C3H7N02 0o. ------·tNH, . .d Aspartic acid C H NO 00_ -.. 1 Asparhc aci (2-aminosuccinic acid) 4 7 4 I 'f ·e- o #IH, ------0 Cysteine Cysteine C3H7N02S Hsyo. +NH, ------;----~~------Cystine Cystine C6H12N20 4S2 HO~s'~o.

------~-----~------0 0 Glutamic acid Glutamic acid C5H9N04 HO~o.

------.~-· Glycine Glycine (aminoacetic acid) C2H5N02 1' ~ 10 ------11'~ Leucine Leucine C6H 13N02 .r...... -y~ 0 Part 3. Phenols and alcohols Common Name IUPACName Molecular Formula Chemical Structure

C 'fi 1 1 h 1 3-(4-Hydroxy-3-methoxyphenyl)- C H 0 CHao~OH om ery a co o 2-propen-l-ol 10 12 3 HO~ ~------2,4-Dimethylphenol 1,3-Dimethyl-4-hydroxybenzene C8H100 )Q:(OH ------OH 3,5-Dimethylphenol 1,3-Dimethyl·S-hydroxybenzene CsH100 16YI m~hyd;o~ybe~~~e--~~oihy&~xyb~~;n;------c;H6o;------;;;~~ci~~------2-Ethylphenol------· or IAY'OH phlorol 1-Ethyl-2-hydroxybenzene C8H100 Qy ~~=~r~hen~r~;--~~;~::~:.::n:------~~;8~------~~------~------Phenol Hydroxybenzene C6H60 ©JOH

~------OH Resorcinol 1,3-Dihydroxybenzene C6H60 2 t6J):

------R e.g., Cholesterol, Campesterol, ~­ Sterols C27H460 to Sitosterol C29HsoO R = H, CH,, C,Hs HO

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Part 4. Carbohydrates Common Name IUPACName Molecular Formula Chemical Structure

Galactose D-Galactose

Glucose D-Glucose C6H120 6 Ho::y.:: ------OH Mannose D-Mannose C6H120 6 HO:x;x·"'OH Ho"'' OH OH Part 5. Aromatic compounds Common Name IUPACName Molecular Formula Chemical Structure

Acenaphthene Acenaphthene

----~------ Anthracene

Benzene Benzene C6H6 ©J Q ------· Benzofluoranthene Benzo[j]fluoranthene C20H12 ~ ;:n:~~~::;:o~:~--:=~~d1:~~~;~~~~n~=:~--~=~~:------~------

Benzonapththo- Benzonapththofluorene (not common in geosphere, synthetic) oooB© ~------

~~~~~~~~:------~~::~:~~~~------::~~~------~------0 Benzopicene Benzo[ a]picene 0 00 00 ~------·

Be!IZ()[a] Benzo[a]pyrene C20H02 ' ------II i

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Part 5. Aromatic compounds, continued Common Name IUPACName Molecular Formula Chemical Structure

Benzo[e]pyrene Benzo[e]pyrene C,.,H, ~ ------Phenylbenzene C,H,. ~

Chrysene C,.H, ~ ------Coronene Coronene C,..H, 0 ------~~~:::::::____ ~~~:::~::~~:::: ______::~~~------~------ Diphenylene oxide C12H80 ~

Diets' hydrocarbon 1,2-(3 '-Methylcyclopenteno )-

Dimethylnaphthalene (1,3-dimethyl isomer Dimethylnaphthalene Ct2H12 ·.~·Q, ', ~Q0 shown; 9 other ~ lQJ..Ql_ ~~e~Y~!~~~------~------:-~------ Ethylbenzene C8H10 ~ Ethylnaphthalene------(1-ethyl isomer. Ethylnaphthalene C12H12 '~ shown; 1 other Isomer .oo: 0 0 possible, i.e., 2-ethyl) • • 00 Eili;t~T~~e------Eili~m~iliylli~~;;;--~------(o-ethyttoluene, · (1-ethyl-2-methylbenzene, c H if ((:)(" if m-ethyltoluene, and 1-ethyl-3-methylbenzene, and 9 12 ~ j ~ ~~~~~l~E~------t~~~:~~~~~~~n~~~l------Fluoranthene Fluoranthene C,J!" ~

Fluorene Fluorene C 13H 10 ~ ------Indan Indan (hydrindene) C9H10 ©:::J

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Part 5. Aromatic compounds, continued Common Name IUPAC Name Molecular Formula Chemical Structure

Indenofluorene Indenofluorene (synthetic)

Indeno[ 1,2,3-cd]- lndeno[ 1,2,3-cd]pyrene ~ pyrene lQt:@ Meili~:c~diliydro:------naphthalene (2-methyl isomer Methyl- I ,2-dihydronaphthalene shown; 7 other :00:' ©V isomers possible) . ------~------4,5-- Cyclopenta[ def]phenanthrene phenanthrene

Methylindan (!-methyl isomer Methylindan C H ·.~.· ~0 shown, three other 10 12 ~ lgU ' ~~~e~y~~~~~------1-Methylnaphthalene 1-Methylnaphthalene

2-Methylnaphtha1ene 2-Methylnaphthalene ------!-Methyl- phenanthrene 1-Methylphenanthrene

Methylstyrene------Methylvinylbenzene (o-methylstyrene, (1-methyl-2-vinylbenzene, c H tQ:(, (Q( $ m-methylstyrene, and 1-methyl-3-vinylbenzene, and 9 10 "( ~~~~~~~~~~t----~~~~~~~~~~~~~~~2------Naphthalene Naphthalene ------Perylene Perylene ~ 00 Phenanthrene Phenanthrene ~ :61' :(gig( f . . l1H-Indeno[2, 1-a] llH-Indeno[2,1-a] ~ phenanthrene phenanthrene CQlJQY""-- J6IOJ ------

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Part 5. Aromatic compounds, continued Common Name IUPACName Molecular Formula Chemical Structure ------Picene Picene C,H,. , ------n-Propylbenzene n-Propylbenzene C9H12 ~ Propylnaphthalene------· (1-propyl isomer -"" r sho~n; 1 .other isomer n-Propylnaphthalene C 13H14 (Q1QJ posstble, I.e., 2- propyl) Prop0~fu~;;------M~h~prop~b~~;n~------(o-propyitoiuene, (1-methyl-2-propylbenzene, C1JI14 ~ ~ ~ m-propyltoluene, and 1-methyl-3-propylbenzene, and ~ 1 ~ ~£~£~~!~~~-----~~~~r~~£~£~~~~~n!L------

Pyrene . Pyrene C1J1 10 ~ ------· Toluene (methylbenzene) C7H8 tQ:( ~------Trimethylbenzene Trimethylbenzene · (hemimellitene, (1,2,3-trimethylbenzene, H c 9 12 rQ( 1Jr" Yo( pseudocumene, and 1,2,4-trimethylbenzene, and l ~ 1 ) 1,3,5-trimethylbenzene) Trimethylnaphthalene------· (1,3,5-trimethyl ~ isomer shown; 13 Trimethylnaphthalene Ct3Ht4 0 0 other isomers possible) ~------· (o-xylene, ~ fAY m-xylene, and Xylene (dimethylbenzene) CgHto ~ cr0 M p-xylene) Part 6. Alkanes and alkenes Common Name IUPACName Molecular Formula Chemical Structure

n-Butane Butane

iso-Butane 2-Methylpropane

1- 1-Butene

2-Butene 2-Butene C4H8 ~ r------ Cyclohexane CoH12 Q ------· n- Decane C10H22 ~ n-Dodecane Dodecane Ethane Ethane

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Part 6. Alkanes and alkenes, continued Common Name IUPACName Molecular Formula Chemical Structure ~------Ethene Ethene C2H4 CH2=CH2

n- Heptane C1H 16 ~ ------~------· n- Hexane C6HI4 ~ ------n-Eicosane Eicosane (icosane) C20H42

Methane Methane CH4 CH4 ------~------· n- Nonane C H ~ ------·9 20 n- Octane CsH 18 ~ n-Pentane Pentane

iso-Pentane 2-Methylbutane neo-Pentane 2,2-Dimethylpropane X ;h~7a~~------~~!!!~!etram~h~~------c:a:------~---­

iris~~~------r.~T~T~Tetram~h~~------c~a~------~------Y~!~~~!~------Propane Propane C3H8 CHrCHrCH3 Propylene------ C H CH -CH=CH ------·3 6 3 2 n-Undecane Undecane C11 H24 ~ Part 7. Biomarkers Common Name IUPACName Molecular Formula Chemical Structure

I ,6-Dimethyl-4.:.isopropyl Cadalene naphthalene ------~

Dehydroabietane Abieta-8, 11, 13-triene ------#

Dehydroabietic acid Abieta~8,11,13-trienoic acid ------~ Dehydroabietin 19-Norabieta-8, 11, 13~triene ~ l I \

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Part 7. Biomarkers, continued Common Name IUPACName Molecular Formula Chemical Structure

------R 5, 14-Dimethyl-l 0, 13-norsteranes Diasteranes (four isomers at each carbon number)

Diploptene 17~(H)-Hop-22(29)-ene

Extended l7a.(H)- 17a(H),21 ~(H)-Homohopanes hopanes (two isomers at each carbon number)

Extended 17~(H)­ 17~(H),21 ~(H)-Homohopanes hopanes (C-22 R configuration only)

Extended tricyclic 14-Alkylcleistanthanes terpanes

~f~"''R 17a.(H)-Hopanes 17a(H),21~(H)-Hopanes S(J~:CH,,~

17~(H)-Hopanes 17~(H),21j3(H)-Hopanes

Moretanes 17~(H),21a.(H)-Hopanes

1-Methyl-7- Retene isopropylphenanthrene

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Part 7. Biomarkers, continued Common Name IUPACName Molecular Formula Chemical Structure

1, 1-Dimethyl-7-isopropyl- Simonellite 1,2,3 ,4-tetrahydrophenanthrene ------R------5a/P(H), 14a(H), 17a(H)-Steranes "'···· 5a/P-Steranes (two isomers at each carbon _, number)

H Part 8. Organosulfur and organonitrogen compounds Common Name IUPACName Molecular Formula Chemical Structure

Benzo[b ]phenanthro Benzo[b ]phenanthro[2, 1- __..,_ -•- J6l6J [2,1-d]thiophene d]thiophene C2oH12S LQI-Jgr ""'

------. 1-Benzothiophene r1\y's) Benzot~wphene (thionaphthene) CsH6S QLJ ------·H Carbazole Carbazole C12H9N ~ ~------Dibenzothiophene Diphenylene sulfide C12H8S ~

Dimethylthiophene------· (2,3-dimethyl isomer Dimethylthiophene C6HsS (•r shown; three other ·o·• 0, ' "---'\ isomers possible) Ethylthiophene------s s (2-ethylthiophene and Ethylthiophene C6H8S Q-\ C(_

Methylbenzothio-~~~r~~~E~~~------~- phene ' s s (2-methyl isomer 2-Methylbenzothiophene C9H8S :©Q: rQ:C.Y shown; 5 other • isomers possible) ------~------Methylethyl disulfide Methylethyldisulfide C3H8S2 CHrCH2-S-S-CH3 Methylpropyl sulfide 1-Methylthiopropane Methylthiophene (2-methylthiophene 2-Methylthiophene (a-thiotolene) C H S and 3-methyl- 5 6 thiophene) ------N Pyridine Pyridine . C5HsN © 1 ------· Quinoline Quinoline C9H7N ©rQJ ~------I Thiophene Thiophene C4H4S Q

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Part 9. Miscellaneous compounds Common Name IUPACName Molecular Formula Chemical Structure ("(0 Cyclohexanone Cyclohexanone C6H100 V ------~~oi~~h0~:;x~~~~henyT------~-~------

Penicillin G acetyl)amino]-4-thia-1-azabi- c,6H!sN204S ~ _/...... , OH cy_clo[3.2.0]heptane-2-carboxylic r()Y'YN yN actd ~ 8 o 0

Note: The suffix (-ic) for a carboxylic acid name is changed to (-ate) to obtain the name ofthe corresponding carboxylate anion.

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Part 9. Miscellaneous compounds Common Name IUPACName Molecular Formula Chemical Structure ("(0 Cyclohexanone Cyclohexanone C6H100 V ------~~oi~~h0~:;x~~~~henyT------~-~------

Penicillin G acetyl)amino]-4-thia-1-azabi- c,6H!sN204S ~ _/...... , OH cy_clo[3.2.0]heptane-2-carboxylic r()Y'YN yN actd ~ 8 o 0

Note: The suffix (-ic) for a carboxylic acid name is changed to (-ate) to obtain the name ofthe corresponding carboxylate anion.

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