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https://hal.archives-ouvertes.fr/hal-03252301; International audience; Summary In the past, highly productive (hyper)saline and alkaline environments have proved propitious for large accumulation of sedimentary OM that led to the formation of Type I kerogens, such as those of the Green River Formation. A sediment core that covers most of the history of Lake Dziani Dzaha, a hypereutrophic saline, alkaline and mostly anoxic crater lakewhich waspostulatedto be a modern analogue of such environments, has been investigated using several analytical approaches comprising bulk (Rock-Eval and C, N, S elemental analyses), isotopic (δ13,14C, δ15N, δ18O, δ33,34,36S), and sedimentological descriptions. This study revealed that, despite strong environmental changes undergone by the lake since its formation, the conditions prevailing in the lake supported by a continuous high primary production have led to an excellent preservation of OM and to early diagenetic reductive and sulfurization processes which have yielded an exceptionally reduced character of the OM with respect to its short diagenetic history (< 6 ky). The similarities observed between the sediments of Lake Dziani Dzaha and some source rocks associated to Type I kerogens suggest that early diagenetic processes can have a strong and rapid impact on the accumulation of OM in some (semi)closed and highly productive aquatic ecosystems.

Summary Four extraction procedures (i.e., Bligh and Dyer, direct acetylation, CH2Cl2/CH3OH extraction and methanolysis) were tested for the recovery of biohopanoids from bacterial cells of a model bacterium (K. xylinus) and yielded similar amounts of bacteriohopanetetrols whatever the procedure used, without significant loss in the aqueous phase in the case of the Bligh and Dyer extraction. In contrast, the recovery of composite bacteriohopanepolyols (cyclitol ether derivatives) was shown to depend on the procedure used, with harsher conditions (i.e., methanolysis and direct acetylation) leading to higher yields. In the case of the Bligh and Dyer extraction, a significant part of the composite biohopanoid pool is lost in the aqueous phase, suggesting that the latter procedure should be avoided if optimal extraction of composite hopanoids is required.

Summary The constitution of Baltic amber, the role of succinic acid and, more generally, of ester bonds in the constitution of macromolecular components of amber has been further investigated by chemical degradation of the solvent insoluble part of Baltic amber using butanolysis (BuOH/HCl). Succinic acid derivatives were the sole compounds released upon butanolysis whereas other compounds which could correspond to the alcohol counterparts of succinates could not be detected by GC-MS. This result indicate that these counterparts are all located on high molecular weight structural moieties. Succinic acid thus plays a key role as cross-linking agent between oligomeric structural moieties based on diterpenoids necessarily bound by at least one non-hydrolysable C-O or C-C bond.

International audience; The tribological performances of engine oils have been shown to be enhanced by the synergistic interactions between Mo dithiocarbamates (Mo(DTC)2) with other additives, and notably Zn dithiophosphates (Zn(DTP)2). Being two key components in formulated lubricants, a detailed understanding of the mechanisms involved between these two types of additives is needed to develop engine oils with enhanced friction reduction performances, and improved fuel economy. In this context, we report here the investigation at the molecular level of the interactions between Mo and Zn complexes with DTC and DTP ligands using laboratory experiments. Our analytical approach comprised NMR spectroscopy (1H, 13C, 31P) allowing direct investigation of both homoleptic and heteroleptic Mo and Zn complexes as well as a specifically-developed HPLC-MS method for the investigation of the different DTC species formed during lubricant ageing experiments. The results showed that ligand exchange reactions between Mo(DTP)2 and Zn(DTC)2 complexes strongly favor the migration of the DTC ligands from Zn to Mo, illustrating the higher affinity of Mo for DTC ligands. In the case of binary mixtures involving Mo(DTC)2 and Zn(DTP)2 – a combination of additives frequently used in formulated lubricants – the formation of mixed complexes (Mo(DTC)(DTP)) resulting from ligand exchange reactions could be directly evidenced for the first time by the analytical methods used. These species could account, at least to some extent, for the synergistic effect of Mo(DTC)2 and Zn(DTP)2 on the friction reducing properties of engine oils. However, they were formed in significantly lower proportions than those previously reported in the literature using indirect methods

International audience; The biomarker distributions of mid-Neoproterozoic sediments (800–717 million yr, Ma) from various locations are characterized by the occurrence, besides cholestane isomers, of a novel series of C28 steranes, whereas classical C-24 alkylated steranes are absent. These unusual C28 steranes, termed cryostanes, seem to be restricted to pre-Snowball Earth sediments. We report their conclusive identification as 26-methyl cholestanes based on comparison of gas chromatographic (GC) behavior and mass spectrum of the last eluting cryostane isomer with those of a 26-methyl 5α(H),14α(H),17α(H),20R-cholestane standard obtained by way of synthesis. Sterols methylated at C-26 seem to be restricted to some demosponges and, based on molecular clock estimates, demosponges may have emerged in the time interval 800–700 Ma. A sponge origin of cryostanes is thereby conceivable, making cryostanes the oldest molecular markers for animals. However, other biological sources need to be explored, including the wide variety of eukaryotic protists.

Birch bark tar, an organic material frequently encountered during archaeological excavations, has been identified from its lipid composition on the cracks of a ceramic dated to the late Neolithic. Lipids of this black substance were dominated by a characteristic triterpenoid assemblage of lupane-related triterpenoids from birch bark, together with their thermal degradation products formed during preparation of the tar. Among the latter, four main series of unusual triterpenoid esters have been detected and were postulated to correspond to esters of Δ 2-betulin and Δ2-dihydrobetulin based on their mass spectra and hydrolysis experiments. Their conclusive identification has been achieved by synthesis of reference compounds. These compounds most likely originate from the esterification between triterpenoid alcohols related to betulin and fatty acids from suberin formed upon heating of birch bark tar. They could be considered as markers of intense heating during birch bark tar preparation using the “single pot” procedure.

The widely distributed aromatic di- and triterpenoids from higher plants occurring in sediments are formed by diagenetic microbial processes affecting their precursor plant lipids. These compounds and their stable isotopic composition (δ13C and δ2H) have the potential to be used for palaeoenvironmental and palaeoclimatic studies. In the present study, the isotopic composition of di- and triterpenoids aromatized to different extents has been measured to specifically examine the isotopic effects associated with the aromatization reaction. To overcome the possibility of multiple higher plant sources, as is generally the case with sedimentary lipids, the δ13C and δ2H values of aromatized di- and triterpenoids from lipid extracts recovered from conifer and angiosperm buried wood have been determined, allowing an unambiguous substrate/product relationship along the aromatization pathway to be assured. The results show that the δ13C compositions of both di- and triterpenes do not seem to be significantly affected by progressive aromatization, whereas the situation is different for δ2H values. In the case of diterpenoids related to abietic acid, a significant increase of the δ2H values by up to 86‰ with ongoing aromatization was measured. This is in contrast to what is expected for dehydrogenated compounds which should be globally more 2H-depleted than their precursor molecules (e.g., biosynthesized unsaturated fatty acids vs. their saturated precursors). This 2H enrichment of aromatized diterpenoids could indicate that they represent only minor residual intermediates, the majority having been further degraded by processes favoring the degradation of the 1H-containing substrates and having a moderately pronounced 12C/13C selectivity. With triterpenoids, preservation of the δ2H values was observed whatever the nature and extent of the aromatization process considered, which may be related to enzymatic reactions showing a limited influence on the hydrogen stable isotopic composition of the aromatized compounds.

International audience; Plant exudates have been extensively used in the past for different applications related to their olfactory, physical or medical properties. Their identification in archaeological samples relies, notably, on the characterisation of chemotaxonomic molecular markers but is often hampered by the severe alteration of their typical genuine molecular signature due to ageing. Among these exudates, those recovered from Styrax, Liquidambar and Myroxylon tree species – defined as balsams – have been exploited in the past for their pleasant scent and medical properties. They are characterised by a large variety of aromatic compounds, especially of the cinnamate and benzoate series, which can be used to assess their botanical source. These compound series may, however, be subject to alteration over time during exposure to environmental conditions in the case of archaeological material. As a result, their reliability as chemotaxonomic markers to characterise and discriminate archaeological balsams is problematic and questionable. We have, therefore, carried out a comparative analysis of various extant balsams (Styrax officinalis, S. paralleloneurum, S. tonkinensis, Liquidambar styraciflua, L. orientalis and Myroxylon balsamum var. pereirae) using gas chromatography–mass spectrometry to search for more solid lipid markers. The results revealed that a distinction between styrax, liquidambars, Peru and Tolu balsams is possible based on the distribution of pentacyclic triterpenes. The predominance of uncommon 6‑oxygenated derivatives of oleanolic acid among triterpenoids could be specifically related to styrax resins. Liquidambar gums were characterised by the predominance of oleanonic acid together with uncommon 3-epi oleanolic and ursolic acids, whereas Peru balsam was rich in cinnamic and benzoic acids, but devoid of triterpenoids. Thanks to the high specificity of some of these triterpenes, already known for their low volatility and robustness towards alteration processes, they should be considered as reliable molecular tools for the unambiguous identification of archaeological balsams. In addition to archaeological applications, these triterpenic markers might also find an application for the detection of counterfeit balsams.

International audience; Deciphering the role of sulfur in biogeochemical cycles strongly relies on its stable isotope composition, which ultimately depends on the ability to quantitatively recover different sulfur species from geological samples. For decades most studies have been restricted to the 34S/32S composition of bulk samples, using simple methods based on the analysis of SO2 released by sample combustion combined to mass spectrometry. The wet chemistry procedures required to selectively extract specific sulfur species were generally avoided due to their tediousness and inefficiency for some complex matrices, especially when targeting organic sulfur. With the recent advent of multi-isotope studies (investigating the minor sulfur stable isotopes 33S and 36S) which rely either on the analysis of sulfur as SF6, or on the use of secondary ion or multi-collector inductively coupled plasma mass spectrometry, wet chemistry-based preparation procedures were brought back to the stage with a renewed interest in developing procedures better adapted to the investigation of specific sulfur species. Here we propose a new stepwise chemical procedure for the quantitative recovery and multi-isotope analysis of organic sulfur from both solvent soluble (total lipid extract) and insoluble (kerogen) fractions, based on a wet oxidation by sodium hypochlorite. This procedure also allows the multi-isotope analysis of inorganic sulfur species (elemental sulfur, sulfates and sulfides) in the same sample. Its application to different well-known petroleum source rocks and to an oil demonstrates its relevance for disentangling the interactions between the different sulfur pools and for shedding new light on the sulfur biogeochemical cycle.

A recent article (Said-Ahmad, W., Amrani, A., Aizenshtat, Z., 2013. The action of elemental sulfur plus water on 1-octene at low temperatures. Organic Geochemistry 59, 82–86) is commented on in this discussion. Radical mechanisms proposed by Said-Ahmad et al. (2013) for the formation of sulfurized and oxidized organic compounds in experiments involving elemental sulfur and 1-octene under aqueous conditions, aimed at investigating the interaction of organic matter and sulfur compounds under geological conditions, are not compatible with their experimental results and other studies. In addition, results from the experiments aimed at demonstrating the role of HO radicals in the formation of oxidized organic compounds were incorrectly interpreted by the authors. In this discussion, alternative mechanisms for the formation of the sulfurized and oxygenated products reported by Said-Ahmad et al. (2013) are proposed.

Euphorbia species are characterized by a net of laticifers producing large amounts of triterpenes. These hydrocarbon-like metabolites can be converted into fuel by the methods of the oil industry. Euphorbia lathyris is easily grown at an industrial scale. In an attempt to increase its triterpene production, the metabolic pathways leading to isoprenoid were investigated by incorporation of 13C labeled glucose and mevalonate and 2H labeled deoxyxylulose as well as by natural abundance isotope ratio GC-MS. Latex triterpenes are exclusively synthesized via the mevalonate (MVA) pathway: this may orient future search for improving the triterpene production in E. lathyris. Phytosterols and their precursors are mainly derived from MVA pathway with a slight contribution of the methylerythritol phosphate (MEP) pathway, whereas phytol is issued from MEP pathway with a minor contribution of the MVA pathway: this is in accordance with the metabolic cross-talk between cytosolic and plastidial compartments in plants. In addition, hopenol B behaved differently from the other latex triterpenes. Its 13C isotope abundance after incorporation of 13C labeled glucose and its natural abundance &delta, 2H signature clearly differed from those of the other latex triterpenes indicating another metabolic origin and suggesting that it may be synthesized by an endophytic fungus.

Maleimides (transformation products of chlorophylls and bacteriochlorophylls) were studied in recent sediments from the Swiss lake Rotsee and the Romanian Black Sea Shelf to investigate chlorophyll degradation, the role of oxygen in maleimide formation, and to identify their sources. Naturally occurring maleimides (i.e. “free” maleimides) and maleimides obtained after chromic acid oxidation of sediment extracts (i.e. “bound” maleimides) were analysed. 2-Methyl-maleimide (Me,H maleimide), 2,3-dimethyl-maleimide (Me,Me maleimide), 2-methyl-3-vinyl-maleimide (Me,vinyl maleimide), 2-methyl-3-ethyl-maleimide (Me,Et maleimide) and traces of 2-methyl-3- iso -butyl-maleimide (Me, i -Bu maleimide) occurred naturally in the sediment with a large predominance of the Me,Et homologue. Tetrapyrrolic pigments related to chlorophylls were the main source of maleimides, although variable contributions of other sources such as cytochromes and/or phycobilins cannot be completely ruled out. The predominant Me,Et maleimide and Me,vinyl maleimide most likely originate mainly from chlorophyll a related pigments. The same holds for Me,H maleimide, which might be formed following degradation of ring E from the tetrapyrrolic nucleus. Alternatively, Me,H maleimide and Me,Me maleimides might be formed by a recently discovered transformation pathway involving the oxidation of vinylic chlorophyll substituents and the formation of an aldehyde intermediate. 2-Methyl-3- n -propyl-maleimide (Me, n -Pr maleimide) and Me, i -Bu maleimide arising from bacteriochlorophyll related pigments traced the presence of phototrophic sulfur bacteria (Chlorobi), indicating photic zone euxinic and anoxic conditions in Rotsee during the last 150 years and throughout the Black Sea history, including the limnic phase of the Black Sea (Unit 3). Some other minor maleimides with specific alkylation pattern also originate from bacteriochlorophylls, while the source of others could not be identified. Free maleimides were mainly formed in the sediment in the absence of oxygen. Novel maleimide degradation indices are proposed to estimate the degree of OM degradation (OM freshness/degradability). These proxies are applicable on longer timescales than e.g. the chlorin index.

The article entitled “Ozonation of triterpenoids: Implications for early diagenesis of biomarkers in oxic environments” (Tay, K.S., Rahman, N.A., Abas, M.R.B, Simoneit, B.R.T., 2013. Organic Geochemistry 57, 34–40) deals with an investigation of the early diagenetic transformations undergone by higher plant triterpenoids under oxic conditions by means of laboratory experiments involving various triterpenes in the presence of ozone. Several aspects of the publication by Tay et al. (2013) are questionable, and are discussed in detail here. These comprise (i) the analytical procedure (based mainly on gas chromatography–mass spectrometry, GC–MS) used for the investigation of reaction mixtures likely to contain thermally labile (poly)oxygenated triterpenoids, (ii) the proposed mechanisms involving the hydroxyl radical as the key oxidizing species, (iii) the interpretation of mass spectra of the products and the structural assignments therefrom, and (iv) the geochemical relevance of the experiments with respect to non-biological oxidative alteration undergone by higher plant triterpenes in sediments.

Samples of young, outer surfaces of brucite-carbonate deposits from the ultramafic-hosted Lost City hydrothermal field were analyzed for DNA and lipid biomarker distributions and for carbon and hydrogen stable isotope compositions of the lipids. Methane-cycling archaeal communities, notably the Lost City Methanosarcinales (LCMS) phylotype, are specifically addressed. Lost City is unlike all other hydrothermal systems known to date and is characterized by metal- and CO2 -poor, high pH fluids with high H2 and CH4 contents resulting from serpentinization processes at depth. The archaeal fraction of the microbial community varies widely within the Lost City chimneys, from 1-81% and covaries with concentrations of hydrogen within the fluids. Archaeal lipids include isoprenoid glycerol di- and tetraethers and C25 and C30 isoprenoid hydrocarbons (pentamethylicosane derivatives - PMIs - and squalenoids). In particular, unsaturated PMIs and squalenoids, attributed to the LCMS archaea, were identified for the first time in the carbonate deposits at Lost City and probably record processes exclusively occurring at the surface of the chimneys. The carbon isotope compositions of PMIs and squalenoids are remarkably heterogeneous across samples and show highly (13) C-enriched signatures reaching δ(13) C values of up to +24.6‰. Unlike other environments in which similar structural and isotopic lipid heterogeneity has been observed and attributed to diversity in the archaeal assemblage, the lipids here appear to be synthesized solely by the LCMS. Some of the variations in lipid isotope signatures may, in part, be due to unusual isotopic fractionation during biosynthesis under extreme conditions. However, we argue that the diversity in archaeal abundances, lipid structure and carbon isotope composition rather reflects the ability of the LCMS archaeal biofilms to adapt to chemical gradients in the hydrothermal chimneys and possibly to perform either methanotrophy or methanogenesis using dissolved inorganic carbon, methane or formate as a function of the prevailing environmental conditions.

We report here a novel reductive coupling reaction of conjugated, non- or poorly enolizable aldehydes induced by H(2) S and operative in aqueous solutions under prebiotically relevant conditions. This reaction leads from retinal to β-carotene, and from benzylic aldehydes to the corresponding diarylethylenes. This novel reaction also opens a new potentially prebiotic pathway leading from glyoxylic acid to various compounds that are involved in the reductive tricarboxylic acid cycle. This C--C bond forming reaction of prebiotic interest might have been operative, notably, in the sulfide-rich environments of hydrothermal vents, which have been postulated as possible sites for the first steps of organic chemical evolution.

Laboratory experiments carried out under plausible prebiotic conditions (under conditions that might have occurred at primitive deep-sea hydrothermal vents) in water and involving constituents that occur in the vicinity of submarine hydrothermal vents (e.g., CO, H(2)S, NiS) have disclosed an iterative Ni-catalyzed pathway of C-C bond formation. This pathway leads from CO to various organic molecules that comprise, notably, thiols, alkylmono- and disulfides, carboxylic acids, and related thioesters containing up to four carbon atoms. Furthermore, similar experiments with organic compounds containing various functionalities, such as thiols, carboxylic acids, thioesters, and alcohols, gave clues to the mechanisms of this novel synthetic process in which reduced metal species, in particular Ni(0), appear to be the key catalysts. Moreover, the formation of aldehydes (and ketones) as labile intermediates via a hydroformylation-related process proved to be at the core of the chain elongation process. Since this process can potentially lead to organic compounds with any chain length, it could have played a significant role in the prebiotic formation of lipidic amphiphilic molecules such as fatty acids, potential precursors of membrane constituents.

The hypothesis of a low temperature natural “vulcanization” process as a potential mechanism for the formation of insoluble bitumen and H2S in reservoirs which have not undergone biodegradation, high thermal stress, or thermochemical sulfate reduction (TSR) has been investigated using laboratory simulation experiments. The experiments, involving elemental sulfur (32S and 34S), a low maturity oil and water at 200 °C in sealed gold tubes, clearly showed that elemental sulfur is able to induce the formation of H2S, polar compounds (resins and asphaltenes) and insoluble bitumen most likely by way of sulfur cross-linking processes. Specific organic sulfur compounds (thiophenes, dithiophenes and thienothiophenes) formed by the reaction of sulfur and hydrocarbons may be potential markers of such a process, but remain to be detected in natural samples.

In order to confirm the tentative structure of a dithiane sulfide with a bicyclic squalene hydrocarbon skeleton representing the predominant alkyl sulfide in Shell Beach samples from the Monterey Formation (Miocene, CA) and also occurring in various immature sulphur-rich sediments [Schouten, S., Sinninghe Damste, J.S., de Leeuw, J.W., 1995. A novel triterpenoid carbon skeleton in immature sulphur-rich sediments. Geochimica et Cosmochimica Acta 59, 953–958], synthesis of a reference compound bearing two thiochromane moieties has been carried out. The product was obtained as a diastereomeric mixture appearing in the form of five peaks (partly) resolved in gas chromatography (GC). This is in sharp contrast with the geochemical compound, which appears as a single broad peak in GC. Co-elution experiments showed that none of the peaks from the synthetic mixture coelute in GC with that of the geochemical sulfide. Furthermore, the different synthetic isomers have identical mass spectra, which are clearly distinct from that of the naturally-occurring compound. The results unambiguously indicate that the natural compound is not the dithiane triterpenoid originally envisaged. Instead, we propose that the compound has a structure of a bicyclic squalene derivative bearing two “S-spiro”-type moieties as is the case for other sulfides related to regular polycyclic polyprenoids and hopanoids in Monterey sediments.

A sulfide with a bicyclic squalene hydrocarbon skeleton present in sediments from various depositional settings and of different geological age has been identified by synthesis of a reference compound. In contrast to previous expectations [cf. Schouten, S., Sinninghe Damste, J.S., de Leeuw, J.W., 1995. A novel triterpenoid carbon skeleton in immature sulphur-rich sediments. Geochimica et Cosmochimica Acta 59, 953–958; Gug, S., Schaeffer, P., Adam, P., Klein, S., Motsch, E., Albrecht, P., 2009. Identification of a sulfide derivative with a bicyclic hydrocarbon skeleton related to squalene. Part I: Synthesis of a dithiane triterpenoid. Organic Geochemistry 40, 876–884.], this sulfide bears two “S-spiro type“ thiolane moities, but not the two thiochromane moieties originally envisaged. The synthesis resulted in the formation of a complex isomeric mixture of compounds, all co-eluting in gas chromatography (GC) in the form of one broad peak, as is the case with the geochemical compound. The spiro-type sulfide was formed by intramolecular sulfurization of a polyunsaturated bicyclic squalene derivative of unknown biological origin. The presence of this sulfide in a number of Triassic to Miocene marine sediments from various and contrasting depositional settings (upwelling environments, shallow continental platforms, lagoonal sub-basins, hypersaline environments), all characterized by strongly anoxic conditions, but with or without photic zone anoxia, indicates that the microorganisms biosynthesizing the precursor bicyclic squalene occupy diverse ecological niches.

The sulfur isotopic composition (δ34S) of petroleum is believed to be affected mainly by sulfur incorporation reactions into the sedimentary organic matter during the early diagenesis. However, secondary processes could affect the original δ34S of oil under the effect of thermal maturity or of the microbial activity of biodegraded reservoirs. In this study, the different processes that may affect the δ34S of in-reservoir oils were assessed based on the sulfur content and isotopes of a series of oil and core samples coming from various reservoirs of the Lower Cretaceous Mannville Group, Western Canada Sedimentary Basin (WCSB). Based on the molecular study, these samples appear to have reached various levels of maturity and biodegradation, ranging from 0 to 6.5 on the biodegradation scale of Peters and Moldowan. In addition, mixing of organic matter coming from different source rocks was identified based on the comparison with extensive correlation studies performed in the WCSB. Investigation of the δ34S shows a trend that seems a priori correlated to the level of biodegradation. However, a careful interpretation of molecular and sulfur isotope data leads to the conclusion that the observed δ34S variations have rather to be ascribed to contributions of oils generated by various source rocks. Alternatively, variations of δ34S could neither be related to maturity differences nor to kinetic effects during organic sulfur compounds biodegradation. In the case of some specific core samples showing a common origin based on biomarker study, δ34S variations might not be related to different sources but to secondary sulfur incorporation/exchange processes occurring within the reservoir. These processes would involve reduced sulfur species from bacterial sulfate reduction formed in situ or migrated into Mannville reservoirs. This hypothesis is supported by laboratory experiments showing sulfur exchange/incorporation under plausible conditions for shallow reservoirs.

Thermochemical sulfate reduction (TSR) is usually associated with significant sour gas (H 2 S) generation and calcite precipitation in deep and hot carbonate reservoirs as a result of reaction between sulfate minerals (primarily anhydrite) and petroleum fluids at elevated temperature (beginning at ∼110-140°C). Thermal enhanced oil recovery (TEOR) techniques are widely applied during production to increase heavy oil recovery in mature fields by lowering oil viscosity. The reservoir rock may reach high temperature (150 °C < T< 300 °C) during steam and hot water flooding for secondary oil recovery that induces TSR. Experimental (pyrolysis in gold tubes) and numerical (0D fluid-rock interaction numerical model: ArXim) simulations were undertaken with a simple petroleum system assimilated to n-alkane model compounds in the presence of sulfate to assess the feasibility of "induced TSR" and to tentatively estimate the sulfur risk in terms of H 2 S and organosulfur compound (OSC) formation during steam and hot water stimulated enhanced recovery operations. The oxidation of organic matter (by reaction with both S° and sulfate) can be easily reproduced under laboratory conditions, as confirmed by the presence of organic sulfur in the soluble and insoluble residue. For the experiments performed in the presence of sulfate, higher amounts of H 2 S, polar compounds and organic residue are produced, and aromatic fractions are enriched in condensed aromatics (sulfur-containing and non-sulfur-containing). Although sulfate reduction from 3% to 5% is deduced from a sulfur balance calculation, no secondary carbonate is detected using X-ray diffraction (XRD). Numerical simulations suggest no limiting thermodynamic factor for the precipitation of carbonate under our experimental conditions and indicate the replacement of sulfate by carbonate. According to numerical data, the lack of carbonate can be explained by its slow growth and/or high energy barrier of nucleation and/or insufficient residence time in laboratory experiments.

We describe the structural elucidation of four novel series of hopanoid sulfides bearing a thiane or a thiolane ring fused to the pentacyclic hopanoid skeleton and the partial identification of an additional spiro-type hopanoid sulfide series which occurs in various immature sulfur-rich sediments and crude oils. These novel diagenetic hopanoid derivatives have been identified either by isolation of one member of the series, followed either by nuclear magnetic resonance (NMR) structural characterization, by synthesis of a reference compound or by deuterium labelling experiments. Location of the C–S bonds between the C-30 or C-31 positions from the side chain and the C-16, C-17, C-20 or C-21 positions in rings D or E of the polycyclic hopanoid skeleton likely indicates that intramolecular sulfurization occurred on precursor molecules functionalized at C-17 and C-21, such as hop-17(21)-ene derivatives, but also, for some of them, at C-16 or C-20. The predominance of one series over the others is variable within the different samples. Their occurrence in a wide variety of sediments and crude oils of different maturity and ranging in age from Triassic to Upper Miocene suggests that the precursor molecules which underwent sulfurization are relatively widespread and that the sulfurization processes involved in their formation are operative during early diagenesis.

The reduction of allylic thiols to alkenes by hydrogen sulfide in aqueous solutions, a novel reaction that may explain reduction processes widely occurring in natural environments, has been discovered. Its mechanism has been studied and suggested to follow an S(RN)1-like pathway involving radical intermediates undergoing 1,4 hydrogen shifts. [reaction: see text]

C30 tetracyclic polyprenoids (TPP) are most prominently observed in samples derived from low salinity, i.e. fresh to brackish lacustrine environments, and are generally present in low levels in samples derived from saline, i.e., marine and saline lacustrine, environments. A near-shore facies of the Chonta Formation, Peru, that has no marine palynomorphs but abundant Chlorococcalean (Green) algal nonmarine palynomorphs, has high levels of TPP, suggesting Green algae (or Chlorophyta) are a possible source for the TPP compounds. The ratio between a C30 TPP compound and 27-norcholestanes is useful for assessing this nonmarine algal input. Moderate elevations of TPP, above what is common in marine derived samples, were found in ostensibly marine source rocks and oils from certain basins of western and northern South America (Middle Magdalena, Colombia; Maracaibo, Venezuela; and Trinidad basins). This is likely due to transport from the nonmarine to the marine environment because of an influx of fresh water into the near-shore marine environment. Alternatively, oils from these basins may have inputs from near-shore shallow marine algae with chemistry similar to that found in lacustrine settings. The TPP ratio, in conjunction with other environmental indicators such as 4-methyl steranes or hopane/sterane ratio, is useful for differentiating marine and nonmarine influences in pre-salt oils and source rocks of West Africa. The TPP ratio, used with other environmental indicators (gammacerane, C29 steranes, C30 steranes) and age diagnostic biomarkers (dinosteranes, 4-methylsteranes), can be useful in differentiating among nonmarine source facies. For example, in the Turpan-Hami basin, China, Permian saline lacustrine and Jurassic lacustrine deltaic facies can be discriminated.

The Be’eri sulfur mine (Israel) is a unique deposit mainly composed of sandstone intercalated with biogenic mats and possessing organic matter exceptionally depleted in 13C. Molecular and isotopic studies of free and bound biomarkers were performed to unravel the source of the organic matter co-occurring with sulfur in this deposit and to propose a paleoenvironmental model of bacterial life in a type of extreme environment. They showed that the biomarkers are all extremely 13C-depleted and almost exclusively composed of hopanoids and biphytane derivatives of bacterial origin, notably methanotrophic bacteria and acidophilic archaea. δ13C values of individual components and of bulk organic carbon are in the −80% to −90% range and are among the lowest values ever measured for hopanoids. Organic matter in the sandstone and the mats differ mainly by the occurrence of 3-methylated hopanoids in the mats, which may reflect either different bacterial populations or different conditions of growth. These data demonstrate that the complete biomass of this deposit primarily derives from methanotrophic hopanoid-synthesizing bacteria consuming methane having seeped toward the surface, and that all other organisms—apparently only archaea and bacteria—must have been thriving on methane-derived carbon (methane, CO2, biomass of methanotrophic bacteria). Unambiguous evidence for photosynthetic organisms in the environment of deposition could not be found. The Be’eri sulfur deposit is thus a fossil remain of an exclusively bacterial ecosystem fueled by methane as sole carbon source and having developed in an interstitial aqueous medium within the sandstone. Elemental sulfur from the deposit probably originates from the oxidation of hydrogen sulfide seeping along with methane, which could have been oxidized either abiotically or biologically by sulfur-oxidizing Beggiatoa-like bacteria and archaea. Further oxidation of elemental sulfur might explain the high acidity of the deposit. The oxidizing conditions now prevailing in the Be’eri deposit were revealed by the occurrence of degraded, oxidized, or thiophenic hopanoid structures. Some of them, unambiguously characterized by synthesis, were also obtained by heating hopenes with elemental sulfur, thus suggesting that the latter could play a role, as dehydrogenating and oxidizing agent, in the transformations undergone by organic matter in the Be’eri deposit.

The biodegradability of macromolecular organic structures of geological origin was investigated by performing in vitro studies. Cultures of the common Nocardioides simplex were grown, first, on a high molecular weight, asymmetric thioether (1-(phytanylsulfanyl)-octadecane 1) and then on macromolecular fractions isolated from a sulfur-rich oil. Gross data indicate that bacteria convert macromolecular substances to material of higher polarity by oxidizing the abundant thioethers to sulfones and sulfoxides and by introducing new functionalities, such as carboxylic acid, keto or hydroxyl groups. Furthermore, bacteria remineralize the macromolecular structures. Bacterially induced alterations were also studied on a molecular level after chemical desulfurization of the macromolecular structure. Thus, it could be established that the amounts of linear hydrocarbons in the macromolecular structure are decreased relative to branched and cyclic structures due to a preferential bacterial attack of the linear moieties bound to the macromolecules. This is further supported by the detection of S-bound fatty acids resulting from the bacterial oxidation of S-bound n-alkanes. Moreover, N. simplex also degraded sulfur-bound steranes by oxidation of the steroid side-chain leading to S-bound steroid acids.

Macromolecular fractions, isolated from the solvent extract of sulfur-rich Recent (Siders Pond, USA; Lake Cadagno, Switzerland; Walvis Bay, Namibia) and immature sediments (Gibellina, Messinian of Sicily; Vena del Gesso, Messinian of Italy), were investigated by chemical degradation using sodium ethanethiolate/methyliodide. This mild reagent which cleaves polysulfide bonds to yield methylsulfides has the advantage over other methods of leaving intact other functionalities (like double bonds) and preserving sulfur atoms at their incorporation site. The method is, therefore, well-suited to the molecular level investigation of sulfur-rich macromolecules from Recent sediments containing highly functionalized polysulfide-bound subunits. In Recent anoxic sulfur-rich sediments, the release of various methylthioethers clearly demonstrates that intermolecular sulfurization of organic matter does occur at the earliest stages of diagenesis. Steroids and phytane derivatives are the major sulfurized lipids, a feature also observed in more mature sulfur-rich sediments. Several phytene derivatives, such as cis and trans 1-methylthiophyt-2-enes, as well as methylthiosteroids, including 5α- and 5β-3-(methylthio)-cholest-2-enes, were identified by comparison with synthesized standards. Steroid methylthioenolethers are released from polysulfide-bound steroid enethiols present in the macromolecular fractions. The latter, which correspond to thioketones, can be considered as intermediates in the reductive sulfurization pathway leading from steroid ketones to polysulfide-bound saturated steroid skeletons and are characterized for the first time in the present study. Thus, it could be shown that the major part of the polysulfide-bound lipids occurring in Recent sediments is apparently the result of sulfurization processes affecting carbonyls (aldehydes and ketones). The unsaturated methylthioethers obtained from Recent sediments were not present in more mature evaporitic samples, which suggests that polysulfide-bound unsaturated thiols are intermediates formed during the first sulfurization steps occurring soon after deposition and that they are rapidly transformed by various processes taking place during early diagenesis, notably to yield their saturated counterparts.

Thioketones have been shown to be likely intermediates in the reduction of ketones and aldehydes to thiols by hydrogen sulfide ions, a reaction which plays an important role in the natural sulfurization of organic matter in sediments. The reduction proceeds by a thiophilic addition of HS− on the thioketone most likely via a single electron transfer mechanism.

High pressure high temperature (HPHT) nanodiamonds (NDs) represent extremely promising materials for construction of fluorescent nanoprobes and nanosensors. However, some properties of bare NDs limit their direct use in these applications: they precipitate in biological solutions, only a limited set of bio-orthogonal conjugation techniques is available and the accessible material is greatly polydisperse in shape. In this work, we encapsulate bright 30-nm fluorescent nanodiamonds (FNDs) in 1020-nm thick translucent (i.e., not altering FND fluorescence) silica shells, yielding monodisperse near-spherical particles of mean diameter 66 nm. High yield modification of the shells with PEG chains stabilizes the particles in ionic solutions, making them applicable in biological environments. We further modify the opposite ends of PEG chains with fluorescent dyes or vectoring peptide using click chemistry. High conversion of this bio-orthogonal coupling yielded circa 2000 dye or peptide molecules on a single FND. We demonstrate the superior properties of these particles by in vitro interaction with human prostate cancer cells: while bare nanodiamonds strongly aggregate in the buffer and adsorb onto the cell membrane, the shell encapsulated NDs do not adsorb nonspecifically and they penetrate inside the cells.

A tetracyclic compound tentatively assigned as A -nor-friedel-8-en-10-one was recently reported by Bakar et al. (2011) [Bakar, N.A., Tay, K.S., Omar, N.Y.M.J., Abas, M.R.B., Simoneit, B.R.T., 2011. Applied Geochemistry 26, 1433–1445] from a Malaysian lake sediment. It was postulated to derive from friedelin via a sequence of diagenetic transformations involving the unprecedented removal of ring A and several hypothetical intermediates. We considered that this structural assignment needed to be reassessed, notably because we could detect the compound in wood samples devoid of friedelin-related triterpenes. Firm identification was also needed since the compound is becoming used as a proxy in recent publications and its occurrence interpreted in terms of palaeoenvironmental reconstruction. In the course of archaeometric studies of ancient buried wood, the presence of the compound as a predominant constituent of the lipid extract of a buried alder wood sample gave us the opportunity to firmly establish its structure. We report here its unambiguous identification using 1D and 2D nuclear magnetic resonance (NMR) spectroscopy after its isolation. Based on its structure, geochemical distribution and stable carbon isotopic composition, it appears that the compound likely does not derive from triterpenoids biosynthesized by higher plants, but might derive from a precursor terpenoid synthesized by microorganisms (bacteria, fungi) living within the buried wood, and possibly involved in the degradation of plant organic matter (wood, notably).

A novel series of unusual A/B diaromatic 14-methylsteroids was identified by total synthesis of reference compound 1a . They constitute the major aromatic hydrocarbon components from Pakistani biodegraded crude oil seeps. They probably derive from the aromatization of ring A functionalized 14-methyl steroid precursors present in green algae.

Several samples from a Tertiary carbonated evaporitic series (Sainte-Cecile, Camargue, France) were investigated. Their analysis revealed a high abundance of new or uncommon hydrocarbons and organic S compounds related to higher plant triterpenes. Several of them, in particular, 12,29-cyclolupa-12,18,20(29)-triene 1, could be positively identified. These triterpenoids are generally absent from non-evaporitic sediments which contain essentially aromatic triterpenoids resulting from microbially mediated aromatization processes starting in ring A (or in ring B when preceded by the loss of ring A). The uncommon transformations undergone by higher plant triterpenes in the highly anoxic sediments from Sainte-Cecile are specific for each series of triterpenes (i.e., oleanane, ursane, lupane) and are probably linked with the rapid disappearance of the functionality located in ring A by reduction or by the incorporation of the triterpenes in S-rich macromolecules by reaction with inorganic S species. These biological markers represent new source parameters which may be quite useful as indicators of terrestrial inputs in evaporitic deposits.

Baccharane (18,19-secolupane) 1, a triterpenoid skeleton seldom encountered in living organisms, has been characterized together with 17βH-des-E-lupane 2, one of its minor degradation products, in Italian Triassic sediment and crude oil samples from the Adriatic Basin by synthesis of standards. Reports of baccharane-derived triterpenoids in the field of natural products are scant and up to now restricted to terrestrial plants (angiosperms and ferns). In this regard, sedimentary baccharane derivatives may indicate a continental contribution (ferns?) to fossil organic matter; but they may also represent a contribution of as yet undetermined marine microorganisms, as has been proposed for dammarenes and dammaranes. Alternatively, they could be the bio/geochemical transformation products of biosynthetically closely related precursors such as lupane- or dammarane-type triterpenoids. The apparently restricted occurrence of baccharane derivatives in geological samples (up to now detected only in Triassic sediments of the Adriatic Basin) confers upon these compounds great value as correlation parameters and possibly as source indicators.

A novel hexane-soluble nonpolar macromolecular fraction (NPMF) has been found to occur in substantial amounts (up to 32%) in sulfur-rich crude oils and a rock extract. It is highly aliphatic and has a molecular weight culminating at several thousand mass units, as proven by spectroscopic and molecular weight studies. C-S bond hydrogenolysis of NPMF with Raney nickel as a catalyst yields high proportions of aliphatic hydrocarbons in which long linear, acyclic polyisoprenoid and carotenoid chains usually predominate (except in one case) over polycyclic structures, such as steroids and hopanoids. Hence, NPMF consists mainly of macromolecules composed of low molecular weight hydrocarbon subunits cross-linked with sulfide bridges. Use of deuterated Raney nickel indicated in one case (Rozel Point oil) that the long chains and some hopanoids are multiattached to the macromolecular network, whereas other structural subunits, such as steroids or gammacerane, are essentially monoattached. Detailed structural determinations of the hydrocarbon “building blocks” of NPMF give information on their origin and the mode of formation of these macromolecules in the subsurface. Indeed, most of the building blocks can be related to algal (e.g., long linear chains, steroids, β-carotene, and related carotenoids) or bacterial (e.g., acyclic and monocyclic carotenoids, long-chain acyclic isoprenoids) precursors which essentially exist in living organisms as monounsaturated or polyunsaturated species or are easily transformed into such species by diagenetic processes (e.g., steroids). It appears that these alkenes or polyenes become selectively trapped into a macromolecular network by reaction with inorganic sulfur species produced by bacteria in a kind of natural, low-temperature, vulcanization process. This process could start at early diagenesis already in the water column or eventually continue in the bottom sediment. Although its exact nature is yet unknown, it seems likely that the cross-linking reaction can be initiated by the cleavage of sulfur species in a radical type mechanism. The alkanes formed upon desulfurization of NPMF usually represent much higher amounts than the free alkanes of the samples and show a dramatically different composition. They may deliver very useful, complementary information in studies related to source and palaeoenvironment.

A novel series of unusual A/B diaromatic 14-methylsteroids was identified by total synthesis of reference compound 1a . They constitute the major aromatic hydrocarbon components from Pakistani biodegraded crude oil seeps. They probably derive from the aromatization of ring A functionalized 14-methyl steroid precursors present in green algae.

A novel thiophene 1 derived from higher plant triterpenoids of the oleanane series was detected in sediments deposited in evaporitic environments and identified by synthesis.

In the course of a detailed palaeoenvironmental study based on biomarker distributions in sediments of Rupelian age (Lower Oligocene from the Rhine Rift Valley), an outcrop sample rich in higher plant fossil remains was collected from a quarry near the city of Burnhaupt-le-Haut (South Alsace, France). In agreement with the macrofossil assemblage, most of the biomarkers were related to terrigenous organic matter, as evidenced by the presence of di- and triterpenoid derivatives from vascular plants. The aromatic hydrocarbon fraction was also shown to contain two predominant series of unknown C 40 oxygenated compounds, as indicated by high resolution mass spectrometry. Isolation of the predominant compound from the first series and of two isomers from the second was undertaken to determine the structures from nuclear magnetic resonance (NMR) studies. Thus, we determined that both series of compounds consist of bis-diterpenoids made up of phenolic sub-units related to totarol and sempervirol, possibly originating from Podocarpaceae. Their formation comprises a first step involving oxidative coupling between the two phenolic monomeric sub-units via a free radical mechanism and leading to the formation of an ether bond (first series of compounds), or a carbon–carbon bond (second series of compounds). In the case of the compounds from the second series, a second, acid-catalysed cyclisation step likely results in the formation of a central dibenzofuranyl moiety. It remains unclear, however, whether these condensation/cyclization mechanisms are biologically-mediated, or result from diagenetic reactions.

A novel series of sedimentary C35 diol and triol hopanoids is reported in a wide range of sediments ranging in age from Recent to Jurassic. The predominant diol homologue has been isolated from a Jurassic sediment using reversed phase HPLC and the structure of the functionalised side chain has been elucidated by 1D and 2D 1H NMR spectroscopy. It corresponds to 32,35-anhydrobacteriohopanetetrol, a compound recently identified in the Caribbean sponge Plakortis simplex. Its widespread occurrence in the sediment record suggests that this novel family of hopanepolyols likely derives from microorganisms which remain to be identified in the bacterial community.

Two bridgehead-alkylated 2-thiaadamantanes (1,5-dimethyl and 1-methyl) have been identified in petroleum; these compounds give clues to sulfurisation processes affecting petroleum which has undergone high thermal stress.

Five series of crude oil samples exposed to atmospheric conditions have been analysed at the molecular level, each series comprising several samples originating from the same crude oil but altered to different extents. The aim of our investigation was to compare the specific impact of abiotic oxidation to other alteration processes such as biodegradation, evaporation and water washing. Bulk analyses revealed that increasing alteration is accompanied by an increase in oxygen content which parallels a relative increase of the proportions, as well as of the molecular weights of the macromolecular constituents of the bitumens. Gas chromatographic–mass spectrometric analyses of polar fractions showed the presence of oxygen-containing compounds (steroid ketones, benzothiophenic acids and sulfones) which result from oxidation of petroleum lipids. The hypothesis that part of these oxygenated compounds results from abiotic oxidation processes rather than from biodegradation is supported, notably, by the fact that oxygen incorporation generally occurred without any diastereomeric discrimination. This is also supported by simulation experiments performed on petroleum lipids, which showed that abiotic oxidation induces cleavage reactions affecting C–C and C–S bonds which may intervene in the transformation of geomacromolecules in the environment by degradation (“depolymerization”). Thus abiotic oxidation may play a major role in the fate of petroleum pollutants in the environment by transforming lipidic organic matter from petroleum into more water soluble and, therefore, more biodegradable constituents. However, these can be more toxic to the environment as the water-soluble fraction may be easily taken up by biota.

Asphaltene samples extracted from archeological and geological bitumens from the Middle East, France, and Spain were studied by sulfur K- and L-edge X-ray absorption near-edge structure (XANES) spectroscopy in combination with isotopic analyses (d 13 C and dD). Within each series, the samples were genetically related by their d 13 C values. The gross and elemental composition and the dD values were used to characterize the weathering state of the samples. Sulfur K- and L-edge XANES results show that in all the samples, dibenzothiophenes are the dominant forms of sulfur. In the least oxidized asphaltenes, minor species include disulfides, alkyl and aryl sulfides, and sulfoxides. With increasing alteration the proportion of oxidized sulfur (sulfoxides, sulfones, sulfonates and sulfates) increases, whereas the disulfide and sulfide content decreases. This evolution is observed in all the series, regardless of the origin of the asphaltenes. This work illustrates the advantages of XANES spectroscopy as a selective probe for determining sulfur speciation in natural samples. It also shows that S K- and L-edge XANES spectroscopy are complementary for identifying the oxidized and reduced forms of sulfur, respectively. Copyright © 1999 Elsevier Science Ltd