Naturally Occurring Allotropes of Carbon.

Carbon is one of the most important chemical elements, forming a wide range of important allotropes, ranging from diamond over graphite to nanostructural materials such as graphene, fullerenes, and carbon nanotubes (CNTs). Especially these nanomaterials play an important role in technology and are commonly formed in laborious synthetic processes that often are of high energy demand. Recently, fullerenes and their building blocks (buckybowls) have been found in natural fossil materials formed under geological conditions. The question arises of how diverse nature can be in forming different types of natural allotropes of carbon. This is investigated here, using modern analytical methods such as ultrahigh-resolution mass spectrometry and transmission electron microscopy, which facilitate a detailed understanding of the diversity of natural carbon allotropes. Large fullerenes, fullertubes, graphene sheets, and double- and multiwalled CNTs together with single-walled CNTs were detected in natural heavy fossil materials while theoretical calculations on the B3LYP/6-31G(d) level of theory using the ORCA software package support the findings.

Physical removal of PAXHs from highly contaminated soil by density differentiation: studying the effectiveness on the molecular level.

Contaminated soils from industrial sites, such as for coal mining or manufactured gas production, can contain polycyclic aromatic hydrocarbons (PAHs) with a concentration higher than 10 000 mg kg-1, which require an integrated approach for remediation. A physical treatment by separating organic contaminants from soil materials using the density difference could lower the cost for the upcoming chemical and/or biological treatment. In our study, a highly PAH contaminated soil was separated in a 39% (w/w) calcium chloride solution (ρ = 1.4 g cm-3) via stirring, aeration or ultrasonication. Both first and second methods could separate soil materials from organic particles efficiently. The light fraction comprised around 10% of the total soil weight but 80% of solvent extractable organics (SEO). Optical and transmission electron microscopic analysis showed the light fraction, which consisted of mainly black solid aggregates (BSA), differed strongly from soil materials. Additionally, the original contaminated soil, its light and heavy fractions and the corresponding water phase together with the manually separated BSA were analyzed on the molecular level using ultrahigh resolution mass spectrometry (HRMS) with different atmospheric pressure ionization (API) methods, such as electrospray (ESI) and atmospheric pressure photo ionization (APPI). Results showed that SEO, which were primarily associated with BSA and successfully separated through physical method, contained mainly condensed aromatic ring structures of pure hydrocarbons and nitrogen heterocycles with low oxygen content.

Chemoselective umpolung of thiols to episulfoniums for cysteine bioconjugation.

Cysteine conjugation is an important tool in protein research and relies on fast, mild and chemoselective reactions. Cysteinyl thiols can either be modified with prefunctionalized electrophiles, or converted into electrophiles themselves for functionalization with selected nucleophiles in an independent step. Here we report a bioconjugation strategy that uses a vinyl thianthrenium salt to transform cysteine into a highly reactive electrophilic episulfonium intermediate in situ, to enable conjugation with a diverse set of bioorthogonal nucleophiles in a single step. The reactivity profile can connect several nucleophiles to biomolecules through a short and stable ethylene linker, ideal for introduction of infrared labels, post-translational modifications or NMR probes. In the absence of reactive exogenous nucleophiles, nucleophilic amino acids can react with the episulfonium intermediate for native peptide stapling and protein-protein ligation. Ready synthetic access to isotopologues of vinyl thianthrenium salts enables applications in quantitative proteomics. Such diverse applications demonstrate the utility of vinyl-thianthrenium-based bioconjugation as a fast, selective and broadly applicable tool for chemical biology.

Investigating Molecular Transformation Processes of Biodiesel Components During Long-Term Storage Via High-Resolution Mass Spectrometry.

Biodiesel is an important building block in renewable energy transformation. The main issue is that during storage biodiesel will undergo transformation processes that can lead to molecular changes, which then can cause applicational problems such as severe motor damage. To prevent this, a detailed understanding of the involved molecules and the emerging aging products is necessary. Biodiesel samples were stored for up to 12 months to monitor molecular changes, and all mixtures were investigated by using ultrahigh-resolution mass spectrometry (HRMS) with electrospray ionization (ESI). The data revealed that during storage large numbers of oxygen atoms were incorporated into the fatty acid methyl esters (FAMEs). This process was dominant for the first quarter of aging but then became overshadowed by dimerization of oxygenated FAMEs. This means that there are two main pathways for aging in biodiesel: polyoxygenation and oligomerization. These findings greatly pin down the possible causes for sedimentation giving a solid foundation for aging inhibition development.

Trash-to-fuel: Converting municipal waste into transportation fuels by pyrolysis.

In daily life humankind is producing a significant amount of garbage, creating a great environmental concern. However, garbage consists of high amounts of carbon based materials, making it a very useful resource. An easy way to use it is to produce transport fuels obtained through pyrolysis. Multiple plastic waste materials were investigated here. Thermogravimetric analysis (TGA) of individual polymers shows that almost complete conversion could be achieved. More than 70% liquid fuels were derived from pyrolysis of polypropylene, polystyrene at 450°C, and low-/high-density polyethylene at 500°C. Using gas chromatography/high-resolution mass spectrometry (GC/HR-MS) allows studying the thermal transformation and proposing a mechanism. An examination of carbon number distribution reveals the potential of plastic liquid fuels, which can be used as an alternative to partial substitution of fossil-fuel-derived gasoline and diesel fuel and also provides a final use of polymer materials, which otherwise would be deposited on waste dumps.

The Ruthenium Nitrosyl Moiety in Clusters: Trinuclear Linear µ-Hydroxido Magnesium(II)-Diruthenium(II), µ3-Oxido Trinuclear Diiron(III)-Ruthenium(II), and Tetranuclear µ4-Oxido Trigallium(III)-Ruthenium(II) Complexes.

The ruthenium nitrosyl moiety, {RuNO}6, is important as a potential releasing agent of nitric oxide and is of inherent interest in coordination chemistry. Typically, {RuNO}6 is found in mononuclear complexes. Herein we describe the synthesis and characterization of several multimetal cluster complexes that contain this unit. Specifically, the heterotrinuclear µ3-oxido clusters [Fe2RuCl4(µ3-O)(µ-OMe)(µ-pz)2(NO)(Hpz)2] (6) and [Fe2RuCl3(µ3-O)(µ-OMe)(µ-pz)3(MeOH)(NO)(Hpz)][Fe2RuCl3(µ3-O)(µ-OMe)(µ-pz)3(DMF)(NO)(Hpz)] (7·MeOH·2H2O) and the heterotetranuclear µ4-oxido complex [Ga3RuCl3(µ4-O)(µ-OMe)3(µ-pz)4(NO)] (8) were prepared from trans-[Ru(OH)(NO)(Hpz)4]Cl2 (5), which itself was prepared via acidic hydrolysis of the linear heterotrinuclear complex {[Ru(µ-OH)(µ-pz)2(pz)(NO)(Hpz)]2Mg} (4). Complex 4 was synthesized from the mononuclear Ru complexes (H2pz)[trans-RuCl4(Hpz)2] (1), trans-[RuCl2(Hpz)4]Cl (2), and trans-[RuCl2(Hpz)4] (3). The new compounds 4-8 were all characterized by elemental analysis, ESI mass spectrometry, IR, UV-vis, and 1H NMR spectroscopy, and single-crystal X-ray diffraction, with complexes 6 and 7 being characterized also by temperature-dependent magnetic susceptibility measurements and Mössbauer spectroscopy. Magnetometry indicated a strong antiferromagnetic interaction between paramagnetic centers in 6 and 7. The ability of 4 and 6-8 to form linkage isomers and release NO upon irradiation in the solid state was investigated by IR spectroscopy. A theoretical investigation of the electronic structure of 6 by DFT and ab initio CASSCF/NEVPT2 calculations indicated a redox-noninnocent behavior of the NO ancillary ligand in 6, which was also manifested in TD-DFT calculations of its electronic absorption spectrum. The electronic structure of 6 was also studied by an X-ray charge density analysis.

Getting a better overview of a highly PAH contaminated soil: A non-targeted approach assessing the real environmental contamination.

Over the last 40 years, soils contaminated with polycyclic aromatic hydrocarbons (PAH) were monitored according to a list of 16 PAH, established by the U.S. Environmental Protection Agency (EPA). This, however, is underestimating the danger to the environment and humanity because other high molecular weight PAHs, heterocycles (PAXH, X = N, O, S) and alkylated derivatives can also occur at the contaminated site. Here, a new non-targeted approach of highly contaminated soil (64.5 ± 9.5 g kg-1 solvent extractable organics from the German Ruhrgebiet) is introduced, where ultrahigh resolution mass spectrometry is combined with multiple ionization methods to get a better overview of anthropogenic contamination at a former industrial site. In total, 21,958 elemental compositions were assigned for positive and negative mode measurements. The approach is strongly increasing the amount of data that can be obtained from a single contaminated soil, making an assessment of the real environmental risk possible. In addition to highly aromatized and (alkylated) high molecular weight PAH, other PAXH especially basic and neutral PANH with very high aromaticity were also detected. This shows that while regulations and routine analysis are still stuck in the 1960 s, modern analytical methods are present in the 21st century.

Flexibilization of Biorefineries: Tuning Lignin Hydrogenation by Hydrogen Partial Pressure.

The present study describes an interesting and practical catalytic system that allows flexible conversion of lignin into aromatic or aliphatic hydrocarbons, depending on the hydrogen partial pressure. A combination of experiment and theory shows that the product distribution between aromatics and aliphatics can be simply tuned by controlling the availability of hydrogen on the catalyst surface. Noticeably, these pathways lead to almost complete oxygen removal from lignin biomass, yielding high-quality hydrocarbons. Thus, hydrogen-lignin co-refining by using this catalytic system provides high flexibility in hydrogen storage/consumption towards meeting different regional and temporal demands.

Studying Natural Buckyballs and Buckybowls in Fossil Materials.

Buckyballs (fullerenes) were first reported over 30 years ago, but still little is known regarding their natural occurrence, since they have so far only been found at sites of high-energy incidents, such as lightning strikes or meteor impacts, but have not been reported in low-energy materials like fossil fuels. Using ultrahigh-resolution mass spectrometry, a wide range of fullerenes from C30 to C114 was detected in the asphaltene fraction of a heavy crude oil, together with their building blocks of C10n H10 stoichiometry. High-level DLPNO-CCSD(T) calculations corroborate their stability as spherical and hemispherical species. Interestingly, the maximum intensity of the fullerenes was found at C40 instead of the major fullerene C60 . Hence, experimental evidence supported by calculations show the existence of not only buckyballs but also buckybowls as 3-dimensional polyaromatic compounds in fossil materials.

Evaluation of the combination of different atmospheric pressure ionization sources for the analysis of extremely complex mixtures.

RATIONALE: Characterization of complex samples remains a challenging task due to the high number of compounds present. Matrix effects, ion discrimination and suppression are limiting factors which force the use of different methods for the same sample to gain a broad understanding of complex mixtures. METHODS: Various ionization techniques such as electrospray ionization (ESI), atmospheric pressure photoionization (APPI) and atmospheric pressure chemical ionization (APCI) have been used in various problems for complex mixture analysis. Especially demanding is the analysis of energy-related hydrocarbon mixtures, such as crude oil. Here, the different ionization sources alone and in combination with each other have been used on an ultrahigh resolution Orbitrap mass spectrometer to study a light crude oil. RESULTS: Despite the great variety of the available ionization sources, there is no single technique which can fully characterize the crude oil. Each ionization technique shows a selectivity towards specific types of compounds. While ESI is the method of choice for the detection of polar compounds, APPI and APCI favor the detection of nonpolar and low-to-medium polar compounds, respectively. The combination of ESI/APPI favors hydrocarbons and oxygen-containing species. CONCLUSIONS: Combining different ionization methods can be used as an alternative in order to gain more information about compounds present in a complex mixture although a combination of different ion sources could enhance suppression effects.

High-resolution GC/MS studies of a light crude oil fraction.

The continuous development in analytical instrumentation has brought the newly developed Orbitrap-based gas chromatography / mass spectrometry (GC/MS) instrument into the forefront for the analysis of complex mixtures such as crude oil. Traditional instrumentation usually requires a choice to be made between mass resolving power or an efficient chromatographic separation, which ideally enables the distinction of structural isomers that is not possible by mass spectrometry alone. Now, these features can be combined, thus enabling a deeper understanding of the constituents of volatile samples on a molecular level. Although electron ionization is the most popular ionization method employed in GC/MS analysis, the need for softer ionization methods has led to the utilization of atmospheric pressure ionization sources. The last arrival to this family is the atmospheric pressure photoionization (APPI), which was originally developed for liquid chromatography / mass spectrometry (LC/MS). With a newly developed commercial GC-APPI interface, it is possible to extend the characterization of unknown compounds. Here, first results about the capabilities of the GC/MS instrument under high or low energy EI or APPI are reported on a volatile gas condensate. The use of different ionization energies helps matching the low abundant molecular ions to the structurally important fragment ions. A broad range of compounds from polar to medium polar were successfully detected and complementary information regarding the analyte was obtained.

Studying the fragmentation mechanism of selected components present in crude oil by collision-induced dissociation mass spectrometry.

RATIONALE: Structural characterization of individual compounds in very complex mixtures is difficult to achieve. One important step in structural elucidation is understanding the mass spectrometric fragmentation mechanisms of the compounds present in such mixtures. Here, different individual compounds presumed to be present in a complex crude oil mixture have been synthesized and structurally characterized by tandem mass spectrometry (MS/MS) studies. METHODS: Model compounds with different aromatic cores and various substitutents were synthesized. Major effort has been put into producing isomerically pure compounds to better understand the fragmentation pattern. Each synthesized compound has been subjected to MSn studies using either a triple quadrupole or a linear ion trap mass spectrometer with electrospray or atmospheric pressure photoionization. The results are used to analyze individual compounds from a complex vacuum gas oil (VGO). RESULTS: The synthesized compounds and a chromatographically simplified vacuum gas oil were used for structural analysis. The major fragmentation mechanism is the benzylic cleavage of the aliphatic side chain. Each side chain can be separately removed from the aromatic core by using MSn methods. At the end of a series of fragmentations, the base aromatic core structure remains and can be chararcterized. CONCLUSIONS: By defining the fragmentation mechanism in complex oil samples it was possible to structurally characterize individual compounds present in a chromatographically simplified VGO. The compounds consist of an aromatic core with aliphatic side chains. Cleavage of all side chains can be achieved by MSn measurements, allowing characterization of the remaining core structure.

Anaerobic degradation of phenanthrene by a sulfate-reducing enrichment culture.

Anaerobic degradation processes are very important to attenuate polycyclic aromatic hydrocarbons (PAHs) in saturated, anoxic sediments. However, PAHs are poorly degradable, leading to very slow microbial growth and thus resulting in only a few cultures that have been enriched and studied so far. Here, we report on a new phenanthrene-degrading, sulfate-reducing enrichment culture, TRIP1. Genome-resolved metagenomics and strain specific cell counting with FISH and flow cytometry indicated that the culture is dominated by a microorganism belonging to the Desulfobacteraceae family (60% of the community) and sharing 93% 16S rRNA sequence similarity to the naphthalene-degrading, sulfate-reducing strain NaphS2. The anaerobic degradation pathway was studied by metabolite analyses and revealed phenanthroic acid as the major intermediate consistent with carboxylation as the initial activation reaction. Further reduced metabolites were indicative of a stepwise reduction of the ring system. We were able to measure the presumed second enzyme reaction in the pathway, phenanthroate-CoA ligase, in crude cell extracts. The reaction was specific for 2-phenanthroic acid and did not transform other isomers. The present study provides first insights into the anaerobic degradation pathways of three-ringed PAHs. The biochemical strategy follows principles known from anaerobic naphthalene degradation, including carboxylation and reduction of the aromatic ring system.

Mechanistic Studies of the Cu(OH)+ -Catalyzed Isomerization of Glucose into Fructose in Water.

The isomerization of glucose to fructose is a crucial interim step in the processing of biomass to renewable fuels and chemicals. This study investigates the copper-catalyzed glucose-fructose isomerization in water, focusing on insights into the roles of the dissolved copper species. Depending on the pH, the thermodynamic equilibrium shifted towards one or a few copper species, namely Cu2+ , Cu(OH)+ , and Cu(OH)2 . According to thermodynamics, the highest concentration of Cu(OH)+ is at pH 5.3, at which the highest fructose yield of 16 % is achieved. The obtained fructose yields strongly correlate with the concentration of Cu(OH)+ . A pH decrease of 2-3 units was observed during the reaction, resulting in the deactivation of the catalyst through hydrolysis in acidic media. Based on the results of the catalytic experiments, as well as spectroscopic and spectrometric studies, we propose Cu(OH)+ as an active Lewis-acidic species following an intramolecular 1,2-hydride shift.

Entropically driven Polymeric Enzyme Inhibitors by End-Group directed Conjugation.

A new generic concept for polymeric enzyme inhibitors is presented using the example of poly(2-methyl-2-oxazoline) (PMOx) terminated with an iminodiacetate (IDA) function. These polymers are shown to be non-competitive inhibitors for horseradish peroxidase (HRP). Mechanistic investigations revealed that the polymer is directed to the protein by its end group and collapses at the surface in an entropy-driven process as shown by isothermal titration calorimetry. The dissociation constant of the complex was determined as the inhibition constant Ki using HRP kinetic activity measurements. Additional experiments suggest that the polymer does not form a diffusion layer around the protein, but might inhibit by inducing minor conformational changes in the protein. This kind of inhibitor offers new avenues towards designing bioactive compounds.

Prophylactic chorioretinectomy for eye injuries with high proliferative-vitreoretinopathy risk.

With its incidence exceeding 60%, proliferative vitreoretinopathy (PVR) remains the most important pathology responsible for loss of vision, even the eyeball, after certain types of severe trauma. In this article, we present results obtained using our novel surgical technique, prophylactic chorioretinectomy (PCR), to prevent the development of PVR. Data on severely injured eyes at high risk for PVR [rupture, posterior laceration, deep-impact intraocular foreign body (IOFB) trauma, perforating injury] were collected prospectively. All eyes underwent vitrectomy (PPV) by PCR within 100 hr of the trauma. Eyes were excluded if they presented with endophthalmitis or if the reconstructive surgery was performed outside this time frame. Forty eyes of 40 consecutive patients were analyzed; full follow-up information was obtained for all of them. The injury was rupture in 27%, penetrating in 15%, (deep-impact) IOFB in 35%, and perforating in 23%. PPV-PCR was performed during primary (wound closure) surgery in 59% of cases. All eyes had at least minimal vitreous hemorrhage, and none had a true posterior vitreous detachment. At the time of PPV, 30% of the eyes had a retinal detachment. Sixteen percent developed PVR, but none from the site of the PCR procedure. In 20%, silicone oil remained in the eye at the last follow-up. The visual acuity improved in 93% of eyes and worsened in none; the improvement was mostly due to surgical clearing of the media opacity. In this subgroup of eyes with severe open-globe trauma, over 60% are expected to develop PVR. PPV/PCR performed within 100 hr reduced the PVR risk significantly, so currently it remains the best option for the surgeon. Clin. Anat. 31:28-38, 2018. © 2017 Wiley Periodicals, Inc.

Quantitative and Qualitative Analysis of Three Classes of Sulfur Compounds in Crude Oil.

Owing to the environmental hazards arising from sulfur-containing combustion products, strong legal regulations exist to reduce the sulfur content of transportation fuels down to a few ppm. With the ongoing depletion of low-sulfur crude oil reservoirs, increased technological efforts are needed for crude oil refining to meet these requirements. The desulfurization step is a critical part of the refining process but partly suffers from the recalcitrance of certain species to sulfur removal and the inability to quantitatively understand the behavior of individual compound classes during the process. We herein present a new and simple approach for the parallel quantification of three different classes of sulfur species present in crude oils by LC separation and on-line detection and quantification by ICP-MS/MS. This approach will help to estimate the amount of recalcitrant species and thus facilitate the optimization of desulfurization conditions during fuel production.

Argentation chromatography coupled to ultrahigh-resolution mass spectrometry for the separation of a heavy crude oil.

Simplification of highly complex mixtures such as crude oil by using chromatographic methods makes it possible to get more detailed information about the composition of the analyte. Separation by argentation chromatography can be achieved based on the interaction of different strength between the silver ions (Ag+) immobilized through a spacer on the silica gel surface and the π-bonds of the analytes. Heavy crude oils contain compounds with a high number of heteroatoms (N, O, S) and a high degree of unsaturation thus making them the perfect analyte for argentation chromatography. The direct coupling of argentation chromatography and ultrahigh-resolution mass spectrometry allows to continuously tracking the separation of the many different compounds by retention time and allows sensitive detection on a molecular level. Direct injection of a heavy crude oil into a ultrahigh-resolution mass spectrometer showed components with DBE of up to 25, whereas analytes with DBE of up to 35 could be detected only after separation with argentation chromatography. The reduced complexity achieved by the separation helps increasing the information depth.

Characterization of crude oil asphaltenes by coupling size-exclusion chromatography directly to an ultrahigh-resolution mass spectrometer.

RATIONALE: Fossil fuels are one of the most important energy resources until new sustainable materials become available. To optimize the upgrading processes of these materials characterization of the remaining heavy materials is of great importance. METHODS: Asphaltenes are the most difficult fraction of crude oil to process due to the limited number of solvents in which they can be dissolved. Chromatographic separation methods need to consider the difficulties associated with these limitations. Size-exclusion chromatography (SEC) in combination with Fourier transform Orbitrap mass spectrometry (MS) combines the capabilities of ultrahigh resolution and very high mass accuracy with a separation method that allows using solvents as mobile phase for asphaltene separation. RESULTS: A chromatographic method was developed that shows the separation of asphaltenes according to their molecular mass. A simplification of the samples was achieved by reducing the number of compounds present in a single spectrum compared to infusion data. Direct detection by mass spectrometry additionally allows a distinction of different isomers present in the complex samples. CONCLUSIONS: Direct coupling of SEC with ultrahigh-resolution mass spectrometry allows the study of the most difficult to analyze fraction of crude oil, the asphaltene fraction. Separation reduces the complexity of individual spectra and, therefore, also reduces suppression and discrimination effects. The separation of structural isomers which cannot be characterized by MS alone gives an added dimension to the analysis of asphaltenes. Copyright © 2016 John Wiley & Sons, Ltd.