Pierre Adam

Structural investigation of nonpolar sulfur cross-linked macromolecules in petroleum

Abstract 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.

Chemical forms of sulfur in geological and archeological asphaltenes from Middle East, France, and Spain determined by sulfur K- and L-edge X-ray absorption near-edge structure spectroscopy

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

Abiotic oxidation of petroleum bitumens under natural conditions

Abstract 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.

Clues to early diagenetic sulfurization processes from mild chemical cleavage of labile sulfur-rich geomacromolecules

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.

An interlaboratory study of TEX86 and BIT analysis of sediments, extracts, and standard mixtures

Two commonly used proxies based on the distribution of glycerol dialkyl glycerol tetraethers (GDGTs) are the TEX86 (TetraEther indeX of 86 carbon atoms) paleothermometer for sea surface temperature reconstructions and the BIT (Branched Isoprenoid Tetraether) index for reconstructing soil organic matter input to the ocean. An initial round-robin study of two sediment extracts, in which 15 laboratories participated, showed relatively consistent TEX86 values (reproducibility +/- 3-4 degrees C when translated to temperature) but a large spread in BIT measurements (reproducibility +/- 0.41 on a scale of 0-1). Here we report results of a second round-robin study with 35 laboratories in which three sediments, one sediment extract, and two mixtures of pure, isolated GDGTs were analyzed. The results for TEX86 and BIT index showed improvement compared to the previous round-robin study. The reproducibility, indicating interlaboratory variation, of TEX86 values ranged from 1.3 to 3.0 degrees C when translated to temperature. These results are similar to those of other temperature proxies used in paleoceanography. Comparison of the results obtained from one of the three sediments showed that TEX86 and BIT indices are not significantly affected by interlaboratory differences in sediment extraction techniques. BIT values of the sediments and extracts were at the extremes of the index with values close to 0 or 1, and showed good reproducibility (ranging from 0.013 to 0.042). However, the measured BIT values for the two GDGT mixtures, with known molar ratios of crenarchaeol and branched GDGTs, had intermediate BIT values and showed poor reproducibility and a large overestimation of the true (i.e., molar-based) BIT index. The latter is likely due to, among other factors, the higher mass spectrometric response of branched GDGTs compared to crenarchaeol, which also varies among mass spectrometers. Correction for this different mass spectrometric response showed a considerable improvement in the reproducibility of BIT index measurements among laboratories, as well as a substantially improved estimation of molar-based BIT values. This suggests that standard mixtures should be used in order to obtain consistent, and molar-based, BIT values.

Fossil bacterial ecosystem at methane seeps: Origin of organic matter from Be’eri sulfur deposit, Israel☆

Abstract 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.

Strong Improvements of Localized Surface Plasmon Resonance Sensitivity by Using Au/Ag Bimetallic Nanostructures Modified with Polydopamine Films

In the present work, the standard monometallic localized surface plasmon resonance (LSPR) biosensing sensitivity is highly improved when using a new system based on glass substrates modified with high-temperature annealed gold/silver bimetallic nanoparticles (Au/Ag bimetallic NPs) coated with polydopamine films before biomolecule specific immobilization. Thus, different zones of bimetallic NPs are spatially created onto a glass support thanks to a commercial transmission electron microscopy (TEM) grid marker in combination with two sequential evaporations of continuous films of gold (4 nm) and silver (2 nm) and followed by annealing at 500 °C for 8 h. By using the scanning electron microscopy (SEM), it is found that annealed Au/Ag bimetallic NPs have uniform size and shape distribution that exhibited a sharper well-defined LSPR resonant peak when compared with that of monometallic Au NPs and thereby contributing to an improved sensitivity in LSPR biosensor application. The controlled micropatterns consisting of bimetallic particles are used in the construction of LSPR biochips for high-throughput detection of different concentrations of a model antigen named bovine serum albumin (BSA) on a single glass sample, with a lower limit of detection of 0.01 ng/mL under the optimized conditions.

Novel aromatic carotenoid derivatives from sulfur photosynthetic bacteria in sediments

Novel aromatic carotenoid derivatives 7 and 8 have been identified by synthesis of reference compounds in a H2/PtO2-hydrogenated fraction from the organic extract of a lake sediment (lake Cadagno, Switzerland). They derive from unreported carotenoids presumably biosynthesized by purple sulfur photosynthetic bacteria (Chromatiaceae) and represent potential biomarkers to establish the occurrence of photic zone anoxia in ancient ecosystems.

A novel series of benzohopanes widespread in sediments

Abstract A novel series (C 31 C 35 ) of benzohopanes cyclized at the C(16) position has been characterized by gas chromatography-mass spectrometry and NMR structural elucidation of the usually predominant C 31 member, the 4′-methylbenzo[16,17,21]-22,29,30-trinorhop-16-ene isolated from the Messel shale (Germany). These biological markers of bacterial origin seem to be widely distributed in sediments and to show low specificity with regard to the depositional environment, although they are well represented in evaporites. Up to now, they have been detected only in thermally immature samples, which could reflect either a relative fragility or other possibilities of transformation as compared to the regular benzohopanes cyclised at C(20).

2α and 3β Steroid thioIs from reductive cleavage of macromolecular petroleum fraction

Cholestane-3β- and 2α-thiol (1 and 2) were identified by synthesis in a fraction of thiols obtained by reductive cleavage with LiAlH4 of di- or polysulfide bridges in a high molecular weight organo-sulfur fraction from a sulfur rich petroleum.