Abstract
Hydrocarbons and lipids are among the most abundant organic compound classes in the biogeosphere. They are formed directly by living organisms as biosynthetic products or through geological transformation of biomass in sedimentary systems. This chapter provides an introduction to the structural diversity of hydrocarbons and lipids and their occurrence in natural environments. Besides saturated, unsaturated, and aromatic hydrocarbons, also selected types of functionalized organic compounds including lipids which play key roles in biogeochemical processes are presented. Important physicochemical parameters are discussed in relation to the structural characteristics of the presented compound classes. For each compound type, reactivity and important reaction types with a special focus on mechanisms relevant to biochemical transformations are presented.
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References
Allred AL (1961) Electronegativity values from thermochemical data. J Inorg Nucl Chem 17:215–221
Ballschmiter K (2003) Pattern and sources of naturally produced organohalogens in the marine environment: biogenic formation of organohalogens. Chemosphere 52:313–324
Ballschmiter K, Schäfer W, Buchert H (1987) Isomer-specific identification of PCB congeners in technical mixtures and environmental samples by HRGC-ECD and HRGC-MSD. Fresenius J Anal Chem 326:253–257
Boll M, Fuchs G, Heider J (2002) Anaerobic oxidation of aromatic compounds and hydrocarbons. Curr Opin Chem Biol 6:604–611
Brown RJC, Brown RFC (2000) Melting point and molecular symmetry. J Chem Educ 77:724–731
Buckel W, Golding BT (2006) Radical enzymes in anaerobes. Annu Rev Microbiol 60:27–49
Curiale JA, Frolov EB (1998) Occurrence and origin of olefins in crude oils. A critical review. Org Geochem 29:397–408
Dahl JE, Moldowan JM, Peters KE, Claypool GE, Rooney MA, Michael GE, Mello MR, Kohnen ML (1999) Diamondoid hydrocarbons as indicators of natural oil cracking. Nature 399:54–57
Dahl JE, Liu SG, Carlson RMK (2003a) Isolation and structure of higher diamondoids, nanometer-sized diamond molecules. Science 299:96–99
Dahl JEP, Moldowan JM, Peakman TM, Clardy JC, Lobovsky E, Olmstead MM, May PW, Davis TJ, Steeds JW, Peters KE, Pepper A, Ehkuan A, Carlson RMK (2003b) Isolation and structural proof of the large diamond molecule, cyclohexamantane (C26H30). Angew Chem 115:2086–2090
de Boer J, de Boer K, Boon JP (2000) Polybrominated biphenyls and diphenyl ethers. In: Paasivirta J (ed) The handbook of environmental chemistry, vol 3. Anthropogenic compounds, Part K. Springer, Berlin, pp 61–96
Evans C, Budwill K, Whiticar M (2020) Geological, geochemical and microbial factors affecting coalbed methane. In: Wilkes H (ed) Hydrocarbons, oils and lipids: diversity, origin, chemistry and fate. Springer International Publishing, Cham. This volume
Favre HA, Powell WH (2013) Nomenclature of organic chemistry. IUPAC recommendations and preferred name 2013. The Royal Society of Chemistry, Cambridge
Ficken KJ, Li B, Swain DL, Eglinton G (2000) An n-alkane proxy for the sedimentary input of submerged/floating freshwater aquatic macrophytes. Org Geochem 31:745–749
Fiedler H (1996) Sources of PCDD/PCDF and impact on the environment. Chemosphere 32:55–64
Fleming FF (1999) Nitrile-containing natural products. Nat Prod Rep 16:597–606
Francke W, Schulz S (1998) Pheromones. In: Mori K (ed) Comprehensive natural products chemistry, vol 8. Pergamon, Oxford, pp 197–261
Gribble GW (1994) The natural production of chlorinated compounds. Environ Sci Technol 28:310A–319A
Gribble GW (2000) The natural production of organobromine compounds. Environ Sci Pollut Res 7:37–49
Grice K, Alexander R, Kagi RI (2000) Diamondoid hydrocarbon ratios as indicators of biodegradation in Australian crude oils. Org Geochem 31:67–73
Hall C, Tharakan P, Hallock J, Cleveland C, Jefferson M (2003) Hydrocarbons and the evolution of human culture. Nature 426:318–322
Hebting Y, Schaeffer P, Behrens A, Adam P, Schmitt G, Schneckenburger P, Bernasconi SM, Albrecht P (2006) Biomarker evidence for a major preservation pathway of sedimentary organic carbon. Science 312:1627–1631
Heider J (2007) Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms. Curr Opin Chem Biol 11:188–194
Hinrichs K-U, Hayes JM, Bach W, Spivack AJ, Hmelo LR, Holm NG, Johnson CG, Sylva SP (2006) Biological formation of ethane and propane in the deep marine subsurface. Proc Natl Acad Sci U S A 103:14684–14689
Horsfield B, Schulz H-M, Bernard S, Mahlstedt N, Han Y, Kuske S (2018) Oil and gas shales. In: Wilkes H (ed) Hydrocarbons, oils and lipids: diversity, origin, chemistry and fate. Springer International Publishing, Cham, pp 1–34
Jarling R, Sadeghi M, Drozdowska M, Lahme S, Buckel W, Rabus R, Widdel F, Golding BT, Wilkes H (2012) Stereochemical investigations reveal the mechanism of the bacterial activation of n-alkanes without oxygen. Angew Chem Int Ed 51:1334–1338
Lide DR (2002) CRC handbook of chemistry and physics, 83rd edn. CRC Press, Boca Raton. 2002–2003
Mango FD (2000) The origin of light hydrocarbons. Geochim Cosmochim Acta 64:1265–1277
Marynowski L, Czechowski F, Simoneit BRT (2001) Phenylnaphthalenes and polyphenyls in Palaeozoic source rocks of the Holy Cross Mountains, Poland. Org Geochem 32:69–85
McMillen DF, Golden DM (1982) Hydrocarbon bond dissociation energies. Annu Rev Phys Chem 33:493–532
Milkov AV (2018) Secondary microbial gas. In: Wilkes H (ed) Hydrocarbons, oils and lipids: diversity, origin, chemistry and fate. Springer International Publishing, Cham, pp 1–10
Peters KE, Walters CC, Moldowan JM (2005) The biomarker guide. Cambridge University Press, Cambridge/New York
Portella G, Poater J, Solà M (2005) Assessment of Clar’s aromatic pi-sextet rule by means of PDI, NICS and HOMA indicators of local aromaticity. J Phys Org Chem 18:785–791
Rabus R, Wilkes H, Behrends A, Armstroff A, Fischer T, Pierik AJ, Widdel F (2001) Anaerobic initial reaction of n-alkanes in a denitrifying bacterium: evidence for (1-methylpentyl)succinate as initial product and for involvement of an organic radical in n-hexane metabolism. J Bacteriol 183:1707–1715
Rabus R, Boll M, Heider J, Meckenstock RU, Buckel W, Einsle O, Ermler U, Golding BT, Gunsalus RP, Kroneck PMH, Krüger M, Lueders T, Martins BM, Musat F, Richnow HH, Schink B, Seifert J, Szaleniec M, Treude T, Ullmann GM, Vogt C, von Bergen M, Wilkes H (2016) Anaerobic microbial degradation of hydrocarbons: from enzymatic reactions to the environment. J Mol Microbiol Biotechnol 26:5–28
Randic M (2003) Aromaticity of polycyclic conjugated hydrocarbons. Chem Rev 103:3449–3606
Schenk HJ, Horsfield B, Krooss B, Schaefer RG, Schwochau K (1997) Kinetics of petroleum formation and cracking. In: Welte DH, Horsfield B, Baker DR (eds) Petroleum and basin evolution. Springer, Berlin, pp 231–269
Schneider-Belhaddad F, Kolattukudy P (2000) Solubilization, partial purification, and characterization of a fatty aldehyde decarbonylase from a higher plant, Pisum sativum. Arch Biochem Biophys 377:341–349
Schoell M (1980) The hydrogen and carbon isotopic composition of methane from natural gases of various origins. Geochim Cosmochim Acta 44:649–661
Seyhan D, Friedrich P, Szaleniec M, Hilberg M, Buckel W, Golding BT, Heider J (2016) Elucidating the stereochemistry of enzymatic benzylsuccinate synthesis with chirally labeled toluene. Angew Chem Int Ed 55:11664–11667
Sinninghe Damsté JS, Strous M, Rijpstra WIC, Hopmans EC, Geenevasen JAJ, van Duin ACT, van Niftrik LA, Jetten MSM (2002) Linearly concatenated cyclobutane lipids form a dense bacterial membrane. Nature 419:708–712
Staudinger H, Ruzicka L (1924) Insektentötende Stoffe I. Über Isolierung und Konstitution des wirksamen Teiles des dalmatinischen Insektenpulvers. Helv Chim Acta 7:177–201
Szaleniec M, Heider J (2016) Modeling of the reaction mechanism of enzymatic radical C-C coupling by benzylsuccinate synthase. Int J Mol Sci 17:514
Taylor P, Larter S, Jones M, Dale J, Horstad I (1997) The effect of oil-water-rock partitioning on the occurrence of alkylphenols in petroleum systems. Geochim Cosmochim Acta 61:1899–1910
Thiele B, Rieder O, Golding BT, Müller M, Boll M (2008) Mechanism of enzymatic birch reduction: stereochemical course and exchange reactions of benzoyl-CoA reductase. J Am Chem Soc 130:14050–14051
Vieth-Hillebrand A, Wilkes H (2020) Stable isotopes in understanding origin and degradation processes of hydrocarbons and petroleum. In: Wilkes H (ed) Hydrocarbons, oils and lipids: diversity, origin, chemistry and fate. Springer International Publishing, Cham. This volume
Wallmann K, Schicks JM (2018) Gas hydrates as an unconventional hydrocarbon resource. In: Wilkes H (ed) Hydrocarbons, oils and lipids: diversity, origin, chemistry and fate. Springer International Publishing, Cham, pp 1–17
Xie S, Lazar CS, Lin Y-S, Teske A, Hinrichs K-U (2013) Ethane- and propane-producing potential and molecular characterization of an ethanogenic enrichment in an anoxic estuarine sediment. Org Geochem 59:37–48
Yunker MB, MacDonald RW, Vingarzan R, Mitchell RH, Goyette D, Sylvestre S (2002) PAHs in the Fraser River basin: a critical appraisal of PAH ratios as indicators of PAH source and composition. Org Geochem 33:489–515
McNaught AD, Wilkinson A (1997) Compendium of chemical terminology, 2nd ed. (the “Gold Book”). Blackwell Scientific Publications, Oxford
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Wilkes, H., Jarling, R., Schwarzbauer, J. (2020). Hydrocarbons and Lipids: An Introduction to Structure, Physicochemical Properties, and Natural Occurrence. In: Wilkes, H. (eds) Hydrocarbons, Oils and Lipids: Diversity, Origin, Chemistry and Fate. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-54529-5_34-1
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DOI: https://doi.org/10.1007/978-3-319-54529-5_34-1
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