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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

1- and 2-photon ionization for online FAIMS-FTMS coupling allows new insights into the constitution of crude oils.

Photoionization techniques (APPI and APLI) are important for the mass spectrometric analysis of crude oils, given the mainly unpolar character of the sample. Ultrahigh resolving Fourier Transform mass spectrometry (FTMS) allows to distinguish between most isobaric compounds as well as to unambiguously determine the elemental compositions of the detected ions. Nevertheless, the complexity of crude oil makes its thorough analysis a difficult task. Besides discriminating effects that can be avoided and depth of information that can be gained by simplification of the sample prior to the MS analysis the presence of numerous isomeric compounds limits the amount of information that can be gained by mass spectrometry alone. Ion mobility spectrometry (IMS) has been shown to be a valuable tool for isomer separation and has also been employed for the analysis of crude oils using IMS-TOF MS. The application of an online FAIMS-FTMS coupling after photoionization for the analysis of crude oils is shown. With this setup the complementarity of data obtained from both APPI and APLI ionization is demonstrated. Online separation and individual detection of different hydrocarbon isomers is achieved.

Functionality, Effectiveness, and Mechanistic Evaluation of a Multicatalyst-Promoted Reaction Sequence by Electrospray Ionization Mass Spectrometry.

A multicatalytic three-step reaction consisting of epoxidation, hydrolysis, and enantioselective monoacylation of cyclohexene was studied by using mass spectrometry (MS). The reaction sequence was carried out in a one-pot reaction using a multicatalyst. All reaction steps were thoroughly analyzed by electrospray ionization (ESI) MS (and MS/MS), as well as high-resolution MS for structure elucidation. These studies allow us to shed light on the individual mode of action of each catalytic moiety. Thus, we find that under the epoxidation conditions, the catalytically active N-methyl imidazole for the terminal acylation step is partially deactivated through oxidation. This observation helps to explain the lower efficiency of the catalyst in the last step compared to the monoacylation performed separately. All reactive intermediates and products of the reaction sequence, as well as of the side-reactions, were monitored, and we present a working mechanism of the reaction.

Selective Analysis of Sulfur-Containing Species in a Heavy Crude Oil by Deuterium Labeling Reactions and Ultrahigh Resolution Mass Spectrometry.

A heavy crude oil has been treated with deuterated alkylating reagents (CD3I and C2D5I) and directly analyzed without any prior fractionation and chromatographic separation by high-field Orbitrap Fourier Transform Mass Spectrometry (FTMS) and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) using electrospray ionization (ESI). The reaction of a polycyclic aromatic sulfur heterocycles (PASHs) dibenzothiophene (DBT), in the presence of silver tetrafluoroborate (AgBF4) with ethyl iodide (C2H5I) in anhydrous dichloroethane (DCE) was optimized as a sample reaction to study heavy crude oil mixtures, and the reaction yield was monitored and determined by proton nuclear magnetic resonance spectroscopy (¹H-NMR). The obtained conditions were then applied to a mixture of standard aromatic CH-, N-, O- and S-containing compounds and then a heavy crude oil, and only sulfur-containing compounds were selectively alkylated. The deuterium labeled alkylating reagents, iodomethane-d3 (CD3I) and iodoethane-d5 (C2D5I), were employed to the alkylation of heavy crude oil to selectively differentiate the tagged sulfur species from the original crude oil.

Online normal-phase high-performance liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry: effects of different ionization methods on the characterization of highly complex crude oil mixtures.

RATIONALE: Characterization of crude oil represents a challenge for researchers due to its complexity. While Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the method of choice for such complex matrices the high number of ions present limits the efficiency of the analysis due to charge competition and space charge effects. One way to solve this problem is the direct coupling of FT-ICR MS with high-performance liquid chromatography (HPLC). METHODS: Normal-phase liquid chromatography was applied on a deasphalted crude oil sample by using a polar aminocyano-bonded stationary phase with n-hexane and isopropyl alcohol as a mobile phase. The HPLC system was coupled online to a 12 T ultrahigh-resolution FT-ICR mass spectrometer. Ion chromatograms were obtained with electrospray ionization (ESI), atmospheric pressure photoionization (APPI), atmospheric pressure chemical ionization (APCI), and atmospheric pressure laser ionization (APLI). RESULTS: The chromatographic separation yielded a group separation into two peaks according to the polarity of the components. Each ionization technique was able to uniquely assign components differing in polarity and aromaticity. Additionally, an increase in aromaticity in the course of retention time for nonpolar species in the first peak was observed. Monitoring the ratio between protonated and radical mono-nitrogen species was achieved. CONCLUSIONS: For the analysis of a crude oil sample, online coupling of a normal-phase HPLC system to an FT-ICR mass spectrometer was achieved. The results of the different ionization techniques were compared with each other, which enables a detailed characterization of the complex sample. Copyright © 2014 John Wiley & Sons, Ltd.

Studying ultra-complex crude oil mixtures by using high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to an electrospray ionisation-LTQ-orbitrap mass spectrometer.

High-field asymmetric waveform ion mobility spectrometry (FAIMS) was coupled directly to an LTQ Orbitrap mass spectrometer to analyze a nitrogen-rich crude oil. Analyzing crude oil is extremely difficult because of the complexity, as up to 100,000 different components can be present. Therefore, simplification of crude oil increases the information content because discrimination and suppression effects are reduced. Here, the first results are presented that show that FAIMS can be an important tool for the simplification of complex mixtures. Additionally, the results show that FAIMS is an excellent tool that allows not only a simplification of such complex mixtures, but also shows the separation of isomeric compounds that have the same elemental composition but different structure and conformation.

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.

Direct coupling of normal-phase high-performance liquid chromatography to atmospheric pressure laser ionization fourier transform ion cyclotron resonance mass spectrometry for the characterization of crude oil.

The high complexity of crude oil makes the use of chromatographic separation an important tool especially for sample simplification. The coupling of normal-phase high-performance liquid chromatography (HPLC) using a polar aminocyano column to a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer offers the best attributes of good separation prior to ultrahigh resolution mass spectrometry (MS) detection. Atmospheric pressure laser ionization (APLI) was used as an ionization technique to analyze the nitrogen-containing aromatic compounds in a deasphalted crude oil due to its unique selectivity toward aromatic compounds and also due to its sensitivity. Two main chromatographic peaks were observed during this separation indicating a class-based separation. Mass spectra obtained from fractions were collected along the entire retention time and compared with each other to assign the unique constituents. By coupling the HPLC system directly to the FTICR mass spectrometer, comparable ion and UV chromatograms were obtained, reflecting the scan-to-scan sensitivity of the coupling system. The results show that it is possible to calculate reconstructed class chromatograms (RCC), allowing differences in class composition to be traced along the retention time. As an example, radical and protonated nitrogen species generated by APLI were detected along the retention time which enabled a differentiation between basic and nonbasic species in the same polar peak, thus overcoming the limitation of chromatographic resolution. This report represents the first online LC-FTICR MS coupling in the field of crude oil analysis.

Impact of different ionization methods on the molecular assignments of asphaltenes by FT-ICR mass spectrometry.

Over the years, ultrahigh resolution mass spectrometry has successfully illustrated the extreme complexity of crude oil and related solubility or polarity based fractions on a molecular level. However, the applied ionization technique greatly influences the outcome and may provide misleading information. In this work, we investigate the atmospheric pressure laser ionization (APLI) technique coupled with Fourier transform ion cyclotron resonance mass spectrometer to analyze the asphaltene fraction of a crude oil. These results were compared to data obtained by using other existing atmospheric pressure ionization methods. Furthermore elemental analysis and solid state NMR were used to obtain the bulk characteristics of the asphaltene sample. The results of the different ionization techniques were compared with the bulk properties in order to describe the potential discrimination effects of the ionization techniques that were observed. The results showed that APLI expands the range of the assigned molecules, while retaining information already observed with the generally used ion sources.

Expanding the data depth for the analysis of complex crude oil samples by Fourier transform ion cyclotron resonance mass spectrometry using the spectral stitching method.

RATIONALE: Crude oil samples are very complex mixtures of compounds and only Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides the ultra-high mass resolution necessary to resolve them. However, FT-ICR MS operates best when only a small amount of ions is present during each transient. This cannot be accomplished with crude oil samples without chromatography because more than 50,000 compounds can be present, with the result that species with low intensity may be suppressed and are detected either with low intensity or not at all. METHODS: Spectral stitching was used to overcome the problems associated with suppression effects, where only short mass windows of 30 amu were scanned to reduce the amount of ions present in each individual scan. Afterwards, all the scans were co-added and the subsequent spectrum was used to calculate individual class distributions. RESULTS: A heavy crude oil sample was analyzed using spectral stitching and this approach was compared with analysis using a broadband-method in order to illustrate the enhancement in depth of information. Although both methods took the same analysis time a seven-times increase in the number of detected species was observed when the spectral stitching method was used compared with the commonly applied broadband method in a 900 amu mass window. CONCLUSIONS: Spectral stitching using smaller selected ion monitoring (SIM) windows for complex crude oil samples allows better class distribution to be obtained because less ion suppression is observed.