Twenty-five years ago, Boduszynski et al. conducted a comprehensive study of heavy oil composition and concluded that crude oil composition increases gradually and continuously with regard to aromaticity, molecular weight, and heteroatom content from the light distillates to non-distillables (the Boduszynski continuum model). Previous exhaustive characterization of heavy vacuum gas oil by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provided compositional data that strongly supports the continuum model. However, when the molecular formulas obtained by FT-ICR MS for the distillates and asphaltenes from the same parent crude oil are plotted as double bond equivalents (DBE) versus carbon number, a gap appears between the compositional space of "asphaltenes" and "maltenes", in contradiction to the Boduszynski−Altgelt model. Here, a heavy distillate cut (atmospheric equivalent boiling point of 523−593 °C) is fractionated according to the number of aromatic rings by HPLC-2. The C7-deasphalted whole oil (C7-DAO), its pentane soluble/insoluble fractions, and each of their ring number fractions are comprehensively characterized by atmospheric pressure photoionization (APPI) FT-ICR MS and tandem mass spectrometry (MS/MS). The HPLC-2 fractions from both the C5-soluble and C5insoluble C7-DAO represent a gradual and continuous progression that fills the compositional "gap" in carbon number and aromaticity between asphaltenes and maltenes as a function of the increasing aromatic ring number, as predicted by Boduszynski. MS/MS results indicate that each ring number fraction comprises both island and archipelago structural motifs. FT-ICR MS reveals a continuum in carbon number and aromaticity. The C5-insoluble C7-DAO components have a similar structure but with higher-order fused ring core structures and are composed of a higher proportion of archipelago structures than the C5-soluble C7-DAO components. Thus, fractionation by the aromatic ring number of "maltenic" and "asphaltenic" species from the C7solubles from a high boiling distillate validates the compositional continuum of petroleum components, and MS/MS exposes the aromatic building blocks of "maltenic" and "asphaltenic" species (structural continuum) that comprise island and archipelago structural motifs.

Of the estimated 5 million barrels of crude oil released into the Gulf of Mexico from the Deepwater Horizon oil spill, a fraction washed ashore onto sandy beaches from Louisiana to the Florida panhandle. Here, we compare the detailed molecular analysis of hydrocarbons in oiled sands from Pensacola Beach to the Macondo wellhead oil (MWO) by electrospray (ESI) and atmospheric pressure photoionization (APPI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to identify major environmental transformation products of polar, high molecular weight (C >25 ) "heavy ends" (high-boiling species) inaccessible by gas chromatography. The petrogenic material isolated from the Pensacola Beach sand displays greater than 2-fold higher molecular complexity than the MWO constituents, most notably in oxygenated species absent in the parent MWO. Surprisingly, the diverse oxygenated hydrocarbons in the Pensacola Beach sediment extracts were dominant in all ionization modes investigated, (±) ESI and (±) APPI. Thus, the molecular-level information highlighted oxygenated species for subsequent "targeted" analyses. First, time-of-flight mass spectrometry analysis of model compounds attributes the unusually large oxygen signal magnitude from positive electrospray to ketone transformation products (O 1 −O 8 classes). Next, negative electrospray mass spectrometry reveals carboxylic acid transformation products. Two-dimensional gas chromatography with mass spectrometry analysis of anion-exchange chromatographic fractions unequivocally verifies the presence of abundant alkyl ketone fragments in sand extracts, and FT-ICR MS analysis reveals the distribution of high-boiling ketone, carboxylic, and higher numbered (3+) oxygen-containing transformation products too polar to be analyzed by gas chromatography. The results expand compositional coverage of oxygen-containing functionalities beyond the classic naphthenic acid type species to complex/mixed ketone, hydroxyl, and carboxylic acid classes of molecules that have been recently identified in produced water, emulsions, and petroleum production deposits.

The mobile proton model (Dongre, A. R., Jones, J. L., Somogyi, A. and Wysocki, V. H. J. Am. Chem. Soc. 1996, 118 , 8365-8374) of peptide fragmentation states that the ionizing protons play a critical role in the gas-phase fragmentation of protonated peptides upon collision-induced dissociation (CID). The model distinguishes two classes of peptide ions, those with or without easily mobilizable protons. For the former class mild excitation leads to proton transfer reactions which populate amide nitrogen protonation sites. This enables facile amide bond cleavage and thus the formation of b and y sequence ions. In contrast, the latter class of peptide ions contains strongly basic functionalities which sequester the ionizing protons, thereby often hindering formation of sequence ions. Here we describe the proton-driven amide bond cleavages necessary to produce b and y ions from peptide ions lacking easily mobilizable protons. We show that this important class of peptide ions fragments by different means from those with easily mobilizable protons. We present three new amide bond cleavage mechanisms which involve salt-bridge, anhydride, and imine enol intermediates, respectively. All three new mechanisms are less energetically demanding than the classical oxazolone b(n)-y(m) pathway. These mechanisms offer an explanation for the formation of b and y ions from peptide ions with sequestered ionizing protons which are routinely fragmented in large-scale proteomics experiments.

a(n) ions are frequently formed in collision-induced dissociation (CID) of protonated peptides in tandem mass spectrometry (MS/MS) based sequencing experiments. These ions have generally been assumed to exist as immonium derivatives (-HN(+)═CHR). Using a quadrupole ion trap mass spectrometer, MS/MS experiments have been performed and the structure of a(n) ions formed from oligoglycines was probed by infrared spectroscopy. The structure and isomerization reactions of the same ions were studied using density functional theory. Overall, theory and infrared spectroscopy provide compelling evidence that a(n) ions undergo cyclization and/or rearrangement reactions, and the resulting structure(s) observed under our experimental conditions depends on the size (n). The a(2) ion (GG sequence) undergoes cyclization to form a 5-membered ring isomer. The a(3) ion (GGG sequence) undergoes cyclization initiated by nucleophilic attack of the carbonyl oxygen of the N-terminal glycine residue on the carbon center of the C-terminal immonium group forming a 7-membered ring isomer. The barrier to this reaction is comparatively low at 10.5 kcal mol(-1), and the resulting cyclic isomer (-5.4 kcal mol(-1)) is more energetically favorable than the linear form. The a(4) ion with the GGGG sequence undergoes head-to-tail cyclization via nucleophilic attack of the N-terminal amino group on the carbon center of the C-terminal immonium ion, forming an 11-membered macroring which contains a secondary amine and three trans amide bonds. Then an intermolecular proton transfer isomerizes the initially formed secondary amine moiety (-CH(2)-NH(2)(+)-CH(2)-NH-CO-) to form a new -CH(2)-NH-CH(2)-NH(2)(+)-CO- form. This structure is readily cleaved at the -CH(2)-NH(2)(+)- bond, leading to opening of the macrocycle and formation of a rearranged linear isomer with the H(2)C═NH(+)-CH(2)- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. This rearranged linear structure is much more energetically favorable (-14.0 kcal mol(-1)) than the initially formed imine-protonated linear a(4) ion structure. Furthermore, the barriers to these cyclization and ring-opening reactions are low (8-11 kcal mol(-1)), allowing facile formation of the rearranged linear species in the mass spectrometer. This finding is not limited to 'simple' glycine-containing systems, as evidenced by the IRMPD spectrum of the a(4) ion generated from protonated AAAAA, which shows a stronger tendency toward formation of the energetically favorable (-12.3 kcal mol(-1)) rearranged linear structure with the MeHC═NH(+)-CHMe- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. Our results indicate that one needs to consider a complex variety of cyclization and rearrangement reactions in order to decipher the structure and fragmentation pathways of peptide a(n) ions. The implications this potentially has for peptide sequencing are also discussed.

b ions are of fundamental importance in peptide sequencing using tandem mass spectrometry. These ions have generally been assumed to exist as protonated oxazolone derivatives. Recent work indicates that medium-sized b ions can rearrange by head-to-tail cyclization of the oxazolone structures generating macrocyclic protonated peptides as intermediates. Here, we show using infrared spectroscopy and density functional theory calculations that the b(5) ion of protonated G(5)R exists in the mass spectrometer as an amide oxygen protonated cyclic peptide rather than fleetingly as a transient intermediate. This assignment is supported by our DFT calculations which show this macrocyclic isomer to be energetically preferred over the open oxazolone form despite the entropic constraints the cyclic form introduces.

Electron-transfer and -capture dissociations of doubly protonated peptides gave dramatically different product ions for a series of histidine-containing pentapeptides of both non-tryptic (AAHAL, AHAAL, AHADL, AHDAL) and tryptic (AAAHK, AAHAK, AHAAK, HAAAK, AAAHR, AAHAR, AHAAR, HAAAR) type. Electron transfer from gaseous Cs atoms and fluoranthene anions triggered backbone dissociations of all four N-C(alpha) bonds in the peptide ions in addition to loss of H and NH(3). Substantial fractions of charge-reduced cation-radicals did not dissociate on an experimental time scale ranging from 10(-6) to 10(-1) s. Multistage tandem mass spectrometric (MS(n)) experiments indicated that the non-dissociating cation-radicals had undergone rearrangements. These were explained as being due to proton migrations from N-terminal ammonium and COOH groups to the C-2' position of the reduced His ring, resulting in substantial radical stabilization. Ab initio calculations revealed that the charge-reduced cation-radicals can exist as low-energy zwitterionic amide pi* states which were local energy minima. These states underwent facile exothermic proton migrations to form aminoketyl radical intermediates, whereas direct N-C(alpha) bond cleavage in zwitterions was disfavored. RRKM analysis indicated that backbone N-C(alpha) bond cleavages did not occur competitively from a single charge-reduced precursor. Rather, these bond cleavages proceeded from distinct intermediates which originated from different electronic states accessed by electron transfer. In stark contrast to electron transfer, capture of a free electron by the peptide ions mainly induced radical dissociations of the charge-carrying side chains and loss of a hydrogen atom followed by standard backbone dissociations of even-electron ions. The differences in dissociation are explained by different electronic states being accessed upon electron transfer and capture.

Most proteins in proteomics are identified from tandem mass spectra of doubly protonated tryptic peptides. Statistical studies indicate that these spectra fall into two distinct classes. IR spectroscopy experiments and DFT calculations performed on model b(2) ions show that peptides producing Class I spectra form protonated oxazolone ions (see figure) and not protonated diketopiperazines as proposed elsewhere.

Graphene represents an attractive two-dimensional carbon-based nanomaterial that holds great promise for applications such as electronics, batteries, sensors, and composite materials. Recent work has demonstrated that carbon-based nanomaterials are degradable/biodegradable, but little work has been expended to identify products formed during the degradation process. As these products may have toxicological implications that could leach into the environment or the human body, insight into the mechanism and structural elucidation remain important as carbon-based nanomaterials become commercialized. We provide insight into a potential mechanism of graphene oxide degradation via the photo-Fenton reaction. We have determined that after 1 day of treatment intermediate oxidation products (with MW 150–1000 Da) were generated. Upon longer reaction times (i.e., days 2 and 3), these products were no longer present in high abundance, and the system was dominated by graphene quantum dots (GQDs). On the basis of FTIR, MS, and NMR data, potential structures for these oxidation products, which consist of oxidized polycyclic aromatic hydrocarbons, are proposed.