Robert M. K. Carlson

Overcoming lability of extremely long alkane carbon-carbon bonds through dispersion forces

Steric effects in chemistry are a consequence of the space required to accommodate the atoms and groups within a molecule, and are often thought to be dominated by repulsive forces arising from overlapping electron densities (Pauli repulsion). An appreciation of attractive interactions such as van der Waals forces (which include London dispersion forces) is necessary to understand chemical bonding and reactivity fully. This is evident from, for example, the strongly debated origin of the higher stability of branched alkanes relative to linear alkanes and the possibility of constructing hydrocarbons with extraordinarily long C–C single bonds through steric crowding. Although empirical bond distance/bond strength relationships have been established for C–C bonds (longer C–C bonds have smaller bond dissociation energies), these have no present theoretical basis. Nevertheless, these empirical considerations are fundamental to structural and energetic evaluations in chemistry, as summarized by Pauling as early as 1960 and confirmed more recently. Here we report the preparation of hydrocarbons with extremely long C–C bonds (up to 1.704 Å), the longest such bonds observed so far in alkanes. The prepared compounds are unexpectedly stable—noticeable decomposition occurs only above 200 °C. We prepared the alkanes by coupling nanometre-sized, diamond-like, highly rigid structures known as diamondoids. The extraordinary stability of the coupling products is due to overall attractive dispersion interactions between the intramolecular H•••H contact surfaces, as is evident from density functional theory computations with and without inclusion of dispersion corrections.

Rearranged hopanes in sediments and petroleum

Abstract Two new rearranged hopanoid hydrocarbons have been isolated from a Prudhoe Bay crude, Alaska. 17α(H)-15α-methyl-27-norhopane was determined by X-ray crystallography. It is the first identified member of a new series of rearranged hopanes we propose to call “17α(H)-diahopanes.” Analysis by gas chromatography-mass spectrometry—mass spectrometry (GC-MS-MS) of the parents of m/z 191 in several crudes suggests that this compound is a member of a C 29 -C 34 series of 17α(H)-diahopanes common to many crude oils and sediments. In addition, a new member of the 18α(H)-neohopane series has also been elucidated. Determination of 18α(H)-17α-methyl-28,30-dinorhopane [18α(H)-30-norneohopane ], which we propose to nickname “C 29 Ts,” hinged upon advanced nuclear magnetic resonance (NMR) techniques (at 500 and 600 MHz) such as proton-detected 1 H- 13 C correlated spectra for the C-skeleton and Rotating-frame Overhauser Enhancement Spectroscopy (ROESY) for stereochemistry, as well as several other two-dimensional (2D) NMR techniques. This compound is the second known pseudohomolog of the neohopane series (together with 18α(H),22,29,30-trisnorneohopane, Ts), but the existence of additional pseudohomologs is still not clear. The structures of these rearranged hopanes are consistent with an origin by catalytic rearrangement from hopenes during early diagenesis. Carbon isotopic data collected on Ts, 17α(H)-diahopane, C 29 Ts, 17α(H)-22,29,30-trisnorhopane (Tm), 17α(H)-30-norhopane, and 17α(H)-hopane isolated from the Prudhoe Bay oil are in the -27 to -28%o δ 13 C range supporting mechanistic arguments based on structures that all are derived from common precursors. These δ 13 C values are slightly more positive than the whole Prudhoe Bay oil (-30.1%), suggesting that these hopanes may have been derived from heterotrophic or cyanobacteria in the paleoecosystem during deposition of its source rock. Molecular mechanics calculations predict relative thermal stabilities in the order 17α(H)-diahopanes > 18α(H)-neohopanes > 17α(H)-hopanes, suggesting new maturity parameters that may be useful into the late oil window.

Sulfur speciation in heavy petroleums: Information from X-ray absorption near-edge structure

Abstract The chemical speciation of sulfur in heavy petroleums, petroleum source rock extracts, and source rock pyrolysis products was studied using X-ray absorption near-edge structure (XANES) spectroscopy. The good energy resolution (ca. 0.5 eV) at the sulfur K edge and the strong dependence of XANES on the sulfur environment combine to give excellent sensitivity to changes in the electronic and structural environment of the sulfur. This has permitted identification and approximate quantitation of different classes of sulfur-containing compounds (e.g., sulfur, sulfides (including disulfides and polysulfides as a group), thiophenes, sulfoxides, sulfones, sulfinic acids, sulfonic acids, and sulfate) in a series of petroleums and petroleum source rocks. Our results indicate that the sulfur speciation of geological samples can be correlated with differences in source depositional environment, thermal maturity, and aromaticity. We report organosulfur compositions for the asphaltene, maltene, and liquid Chromatographie fractions of two sulfur-rich oils. In addition, we find that the organosulfur species in some, but not all, oils are subject to oxidation upon storage and thus may also be susceptible to oxidation in shallow reservoirs exposed to oxic waters. This work illustrates the utility of XANES as a direct spectroscopic probe for the quantitative determination of sulfur species in geological samples.

Minor and trace sterols in marine invertebrates: VI. Occurrence and possible origins of sterols possessing unusually short hydrocarbon side chains☆

Abstract Sterols with biosynthetically unusually short side chains (fewer than eight carbon atoms expected for primary squalene cyclization products) have been identified in the extracts of numerous marine invertebrates. The structures of the short side chain and conventional side chain sterols have been determined for various species of Porifera and Coelenterata. Sterol structures were determined by comparison of their mass spectra and gas chromatographic retention times with those of authentic or synthetic samples. Evidence is presented supporting the natural occurrence of these compounds in the tissues of the marine invertebrates as opposed to formation by degradative processes during sample handling or laboratory work-up. The short side chain sterols were found to possess predominantly the androst-5-en-3β-ol nucleus with C-17 alkyl side chains ranging from zero to six carbon atoms. Concentrations of short side chain sterols range from trace levels to over 5% of the sterol mixture in various species. The possible origins of these short side chain sterols are evaluated in the light of current knowledge of sterol function, biosynthesis, dealkylation, microbial degradation, and autoxidation. Known sterol autoxidations are reviewed, and possible singlet oxygen and free radical mechanisms of sterol side chain autoxidation (at physiological temperatures) which may lead to sterols with shortened hydrocarbon side chain are suggested. The possible autoxidative generation of short side chain sterols from known marine sterols by the suggested mechanisms is evaluated through application of the REACT computer program. Predicted short side chains are tabulated for each parent marine sterol side chain and then compared with the compositions of the actual sterols found in the marine extracts examined. The possible natural environmental or in vivo autoxidative formation of the short side chain marine sterols is supported by these evaluations.

Minor and trace sterols in marine invertebrates 1. General methods of analysis

3beta-Hydroxy sterols occurring at a concentration of at least 0.001% of the sterol mixtures of Pseudoplexaura porosa and Plexaura homomalla have been fractionated using a series of refined techniques and subsequently analyzed using combined gas chromatography-mass spectrometry (GC-MS) in the development of a procedure for examining the minor and trace components of marine sterol mixtures. A total of 49 sterols were found which spanned a molecular weight range of 274 to 440. In addition delta4-3-keto analogs of cholesterol, 24-methylcholesterol and gorgosterol were found in the extracts of P. homomalla. Initial separation of various natural sterol-containing conjugates and free sterols was found to have a number of advantages. Fractional digitonin precipitation and alumina column chromatography were found to possess greater sterol separation abilities than previously recognized. Many of the minor sterols were found to possess novel structures including a series of short side chain sterols, 19-nor sterols, 5beta-stanols and 4-monomethyl sterols for which structure elucidation work is continuing.

Carbon isotopic composition of individual biomarkers in gilsonites (Utah)

Carbon isotopic compositions of saturated hydrocarbon, aromatic hydrocarbon, NSO (resin), and asphaltene fractions of vein-forming gilsonites (Cowboy, Bonanza, Independence, Wagonhound and Harrison veins) in the NE Uinta Basin, Utah, are all similar and isotopically resemble Mahogany Zone shale extracts of the Green River Formation (δ 13C ∼ −29 to −31%). Individual molecular fossils in the gilsonites show a wider variability in compositions indicative of their paleoecological origins within the Eocene Uinta/Greater Green River paleolake system. Carbon isotopic compositions of C28 and C29 steranes (δ 13C = −25 to −32%), pristance and phytane (−33 to —34%) and perhydroβ-carotene (carotane) (δ 13C = −33.2%) suggest that organisms producing these compounds grew near the lake surface. The C33 carotenoid, lexane, is isotopically identical to the C40 carotenoid, carotane, supporting a common C40 carotenoid precursor. Two groups of hopanes can be differentiated in the gilsonites based on carbon isotopic compositions: C29, C31 and C32 hopanes and moretanes (−40.9 to −44.3%), consistent with a source from midwater bacteria and C30 hopanes and moretanes (−51.0 and −60.5%) for which the strong 13C depletion suggests at least partial derivation from methylotrophs. The isotopic signatures of these molecular fossils suggest the source beds of the gilsonites were deposited in a stratified paleolake system with a depositional environment similar to that which formed the Mahogany Zone shales of the Piceance Creek Basin. Algal biomarkers in the gilsonites are isotopically uniform throughout the area of the gilsonite vein occurrence (∼1500 km3) and resemble those in the Mahogany Zone shale in the Piceance Creek Basin over 50 km to the East. This remarkable lateral uniformity suggests that very similar photic zone water conditions existed across the entire Uinta/Piceance Creek paleolake system at the time of deposition of the gilsonite source bed (Mahogany Zone shale). Sterane isotopic compositions are effective for the genetic correlation of the solid bitumens/immature oils. In contrast, the carbon isotopic compositions of the bacterial biomarkers in the gilsonites vary significantly, suggesting that conditions in deeper waters of the paleolake system were more variable. Carbon isotopic signatures of individual hopane biomarkers, in the Green River formation, appear to be valuable for identifying different source facies characteristics within the same paleolake depositional system.

Spatially resolved electronic and vibronic properties of single diamondoid molecules

Diamondoids are a unique form of carbon nanostructure best described as hydrogen-terminated diamond molecules. Their diamond-cage structures and tetrahedral sp3 hybrid bonding create new possibilities for tuning electronic bandgaps, optical properties, thermal transport and mechanical strength at the nanoscale. The recently discovered higher diamondoids have thus generated much excitement in regards to their potential versatility as nanoscale devices. Despite this excitement, however, very little is known about the properties of isolated diamondoids on metal surfaces, a very relevant system for molecular electronics. For example, it is unclear how the microscopic characteristics of molecular orbitals and local electron-vibrational coupling affect electron conduction, emission and energy transfer in the diamondoids. Here, we report the first single-molecule study of tetramantane diamondoids on Au(111) using scanning tunnelling microscopy and spectroscopy. We find that the diamondoid electronic structure and electron-vibrational coupling exhibit unique and unexpected spatial correlations characterized by pronounced nodal structure across the molecular surfaces. Ab initio pseudopotential density functional calculations reveal that much of the observed electronic and vibronic properties of diamondoids are determined by surface hydrogen terminations, a feature having important implications for designing future diamondoid-based molecular devices.

Geochemical comparison of reservoir solid bitumens with diverse origins

Abstract Geochemical and petrologic comparison of solid bitumens with various origins from reservoirs in Zaire, Canada and Kazakhstan were studied to provide insight into their formation processes and their physical and chemical properties. Results of this study can help develop methods for treatment and removal of solid bitumen, and evaluating producibility of associated hydrocarbon fluids. Characterization of these solid bitumens reveals a wide range in quantity and composition of extractables (soluble material) and in solid bitumen reflectance, which indicate significant differences in formation processes, hydrocarbon source and thermal maturity. The Zaire and Kazakhstan samples represent end members of the spectrum of solid bitumens studied. Solid bitumens from the Motoba Field, Zaire, are highly extractable and low in thermal maturity (0.2 – 0.3% bitumen reflectance). Reservoir mixing of a Cretaceous lacustrine sourced oil and a Tertiary marine sourced oil of different thermal maturities appears to be responsible for their formation. In contrast, solid bitumens from the Tengiz Field, Kazakhstan, are characterized by their extremely low extractables, high bitumen reflectance (> 1%) and low atomic H/C ratios (

Synthesis of Higher Diamondoids and Implications for Their Formation in Petroleum

triamantane (3) and so forth, can be prepared by chemical synthesis. Of the higher diamondoids, i.e., those that have isomeric forms, only C2h-symmetric [121]tetramantane (4 a) has been prepared in the laboratory in very low yields. All other higher diamondoids are only accessible from raw petroleum. There are three tetramantanes (4a and [1(2)3]tetramantane, C3v-4b ) including one enantiomeric pair (P)-(+)and (M)-( )-[123]tetramantane (4c), six pentamantanes (with [1(2,3)4]pentamantane being the first exhibiting a diamond {111} surface), 24 hexamantanes (6), 12] nearly one hundred heptamantanes (7), and so forth. Thus far, diamondoids with up to 11 cages have been shown to exist in petroleum, but no other source is known, although recent studies suggest possible interstellar occurrence. The larger nanodiamonds occur as rigid rods (4a, 5c), discs (4b), 12] pyramids (5 a), and helices (4c, 5 f), exhibiting quantum confinement and negative electron affinity. They can be specifically derivatized, 11,17, 18] with electron emission properties superior to any other material making them attractive for molecular electronics. The mechanism for formation of these nanodiamonds for a long time was attributed to thermodynamically controlled carbocation rearrangements. 21] Such mechanisms enable the practical synthesis of 1–3 but they fail in the production of the higher diamondoids. 21, 22] A detailed analysis of the mechanism for adamantane formation from a single starting material shows an amazing 2897 pathways; a more limited analysis of triamantane formation through carbocation pathways indicates at least 300000 potential intermediates. Prospects for higher diamondoid syntheses by these pathways are bleak due to a lack of large polycyclic precursors, problems with intermediates trapped in local energy minima, disproportionation reactions leading to side products, and the exploding numbers of isomers as the size of target higher diamondoid products increases. With the failure of syntheses of higher diamondoids through carbocation rearrangements, attempts at their preparation were abandoned in the 1980s. Since higher diamondoids occur in relatively high concentrations in petroleum that has undergone thermal cracking (i.e., been subjected to very high temperatures due to deep burial), we began to consider that these free-radical cracking reactions might be involved in higher diamondoid formation. The uncatalyzed formation of 1 and 2 from n-alkanes under conditions of cracking was shown recently, presenting evidence that exclusively thermal pathways involving free radicals can readily compete with the typically assumed acidcatalyzed carbocation rearrangements. Such mechanistic proposals underline the notion that diamondoids are thermodynamically the most stable hydrocarbons, i.e., they are more stable than nanographenes (extended polycyclic aromatic hydrocarbons) of comparable molecular weight. Moreover, the relative stabilities of carbocations and alkyl radicals Scheme 1. The family of diamondoids: lower diamondoids 1–3, the three isomers of tetramantane (4), and the six pentamantanes (5). The numbers in brackets refer to the unique Balaban–Schleyer nomenclature.

Infrared Spectroscopy of Diamondoid Molecules: New Insights into the Presence of Nanodiamonds in the Interstellar Medium

Although they are relatively different in band shape, infrared features around 3.4-3.5 μm in the emission spectra of HD 97048 and Elias 1 and in the absorption spectra of various dense clouds have both been attributed to diamondoid molecules/particles. This assignment is based mainly on infrared spectra of hydrogenated diamond thin films and of diamond nanocrystals of known average size. Here we present an analysis of the astrophysical implications of recently reported solid-state 2.5-12.5 μm spectra of individual diamondoid molecules, up to the size of hexamantane (C26H30). These spectra provide the first experimental measurements of the infrared frequencies of this class of molecules. In addition, laboratory gas-phase infrared emission spectra of the three smallest members of the diamondoid family are reported, as well as theoretical spectra for some larger species. The present data set allows us to relate spectral signatures to the molecular size and structure. The spectra of tetrahedral diamondoids are found to be qualitatively different from those of lower symmetry species, which possibly explains the differences between the astrophysical emission and absorption spectra. Interestingly, the 3.53 μm band is clearly observed in the spectra of these small molecular diamondoids, whereas previous studies on nanodiamond particles found this band only for species larger than ≈50 nm. Our results support the assignment of the 3.43 and 3.53 μm emission features in HD 97048 and Elias 1 to diamondoids of a few nanometers in size as well as the suggestion that smaller diamondoid molecules contribute to the 3.47 μm interstellar absorption band.