Tandem mass spectrometry of electrospray ionized multiply charged peptide ions is commonly used to identify the sequence of peptide(s) and infer the identity of source protein(s). Doubly protonated ...peptide ions are consistently the most efficiently sequenced ions following collision-induced dissociation of peptides generated by tryptic digestion. While the broad characteristics of longer (N ≥ 8 residue) doubly protonated peptides have been investigated, there is comparatively little data on shorter systems where charge repulsion should exhibit the greatest influence on the dissociation chemistry. To address this gap and further understand the chemistry underlying collisional-dissociation of doubly charged tryptic peptides, two series of analytes (G x R+2H2+ and A x R+2H2+, x = 2–5) were investigated experimentally and with theory. We find distinct differences in the preference of bond cleavage sites for these peptides as a function of size and to a lesser extent composition. Density functional calculations at two levels of theory predict that the threshold relative energies required for bond cleavages at the same site for peptides of different size are quite similar (for example, b2-yN‑2). In isolation, this finding is inconsistent with experiment. However, the predicted extent of entropy change of these reactions is size dependent. Subsequent RRKM rate constant calculations provide a far clearer picture of the kinetics of the competing bond cleavage reactions enabling rationalization of experimental findings. The M06-2X data were substantially more consistent with experiment than were the B3LYP data.
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 C5-insoluble 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 C7-solubles 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.
Most photodynamic therapeutics (PDTs) used in cancer treatment require oxygen to work efficiently to terminate cancer cells. These PDTs do not efficiently treat tumors in hypoxic conditions. Rh(III) ...polypyridyl complexes have been reported to have a photodynamic therapeutic effect in hypoxic conditions when exposed to UV light. UV light can damage tissue and cannot penetrate deep to reach cancer cells. This work proposes the coordination of a BODIPY fluorophore to a rhodium metal center to form a Rh(III)-BODIPY complex that enhances the reactivity of the rhodium under visible light. This complex formation is facilitated with the BODIPY as the highest occupied molecular orbital (HOMO), while the lowest unoccupied molecular orbital (LUMO) is localized on the Rh(III) metal center. Irradiation of the BODIPY transition at ∼524 nm can cause an indirect electron transfer from the orbital of the BODIPY-centered HOMO to the Rh(III)-centered LUMO, populating the dσ* orbital. In addition, photo binding of the Rh complex covalently coordinated to the N (7) position of guanine in an aqueous solution was also observed by mass spectrometry after chloride dissociation upon irradiation with green visible light (532 nm LED). Calculated thermochemistry values of the Rh complex reaction in methanol, acetonitrile, water, and guanine were determined using DFT calculations. All enthalpic reactions and Gibbs free energies were identified as endothermic and nonspontaneous, respectively. This observation supports the chloride dissociation using 532 nm light. This Rh(III)-BODIPY complex expands the class of visible light-activated Rh(III) photocisplatin analogs that may have potential photodynamic therapeutic activity for the treatment of cancers in hypoxic conditions.
Gas-Phase Dissociation Chemistry of Deprotonated RGD Guan, Shanshan; Rabus, Jordan M; Maître, Philippe ...
Journal of the American Society for Mass Spectrometry,
01/2021, Letnik:
32, Številka:
1
Journal Article
Recenzirano
We investigate the structure and dissociation pathways of the deprotonated amphoteric peptide arginylglycylasparic acid, RGD-H
. We model the pertinent gas-phase structures and fragmentation ...chemistry of the precursor anions and predominant sequence-informative bond cleavages (
,
, and
peaks) and compare these predictions to our tandem mass spectra and infrared spectroscopy experiments. Formation of the
anions requires rate-limiting intramolecular back biting to cleave the second amide bond and generate an anhydride structure. Facile cleavage of the newly formed ester bond with concerted expulsion of a cyclic anhydride neutral generates the product structure. IR spectroscopy supports this
anion having structures that are essentially identical to C-terminally deprotonated arginylglycine, RG-H
. Formation of the
anion is predicted to require concerted expulsion of CO
from the aspartyl side chain carboxylate and cleavage of the N-C
bond to produce a proton-bound dimer of arginylglycinamide and acrylate. Proton transfers within the dimer then enable predominant detection of a
anion with the negative charge nominally on the central, glycine nitrogen (amidate structure) as the proton affinity of this structure is predicted to be lower than acrylate by ∼27 kJ mol
. Alternate means of cleaving the same N-C
bond produce deprotonated
-1,4-dibut-2-enoic acid
anion structures. These lowest energy processes involve C-H proton mobilization from the aspartyl side chain prior to N-C
bond cleavage consistent with proposals from the literature.
We characterize the primary fragmentation reactions of three isomeric lithiated D-hexose sugars (glucose, galactose, and mannose) utilizing tandem mass spectrometry, regiospecific labeling, and ...theory. We provide evidence that these three isomers populate similar fragmentation pathways to produce the abundant cross-ring cleavage peaks (
0,2
A
1
and
0,3
A
1
). These pathways are highly consistent with the prior literature (Hofmeister et al. J. Am. Chem. Soc.
113
, 5964–5970,
1991
, Bythell et al. J. Am. Soc. Mass Spectrom.
28
, 688–703,
2017
, Rabus et al. Phys. Chem. Chem. Phys.
19
, 25643–25652,
2017
) and the present labeling data. However, the structure-specific energetics and rate-determining steps of these reactions differ as a function of precursor sugar and anomeric configuration. The lowest energy water loss pathways involve loss of the anomeric oxygen to furnish B
1
ions. For glucose and galactose, the lithiated α-anomers generate ketone structures at C2 in a concerted reaction involving a 1,2-migration of the C2-H to the anomeric carbon (C1). In contrast, the β-anomers are predicted to form 1,3-anhydroglucose/galactose B
1
ion structures. Initiation of the water loss reactions from each anomeric configuration requires distinct reactive conformers, resulting in different product ion structures. Inversion of the stereochemistry at C2 has marked consequences. Both lithiated mannose forms expel water to form 1,2-anhydromannose B
1
ions with the newly formed epoxide group above the ring. Additionally, provided water loss is not instantaneous, the α-anomer can also isomerize to generate a ketone structure at C2 in a concerted reaction involving a 1,2-migration of the C2-H to C1. This product is indistinguishable to that from α-glucose. The energetics and interplay of these pathways are discussed.
Graphical Abstract
ᅟ
Liquid chromatography–mass spectrometry (LC-MS) based metabolomics suffers from extended duty cycles and matrix-dependent quantitation. Chemical tags with 96 unique masses are reported, which ...alleviate the metabolomic workflow bottleneck and allow for absolute quantitation. A metabolic screen for carboxylic acids was performed on mammalian cells deprived of various nutrients and showed 24% RSD and analysis of 288 samples in 2 h.
Discovery and identification of a new endogenous metabolite are typically hindered by requirements of large sample volumes and multistage purifications to guide synthesis of the standard. Presented ...here is a metabolomics platform that uses chemical tagging and tandem mass spectrometry to determine structure, direct synthesis, and confirm identity. Three new homocysteine metabolites are reported: N-succinyl homocysteine, 2-methyl-1,3-thiazinane-4-carboxylic acid (MTCA), and homolanthinone.
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.
Recently, I explored structurally straightforward pathways to Cα hydrogen atom, H•, transfer reactions in the radical cation complex following electron capture/transfer of a series of polyprotonated ...peptides (J. Phys. Chem. A 2013, 117, 1189–1196). Here, I extend my analysis to incorporate detailed rearrangement processes potentially occurring prior to H• transfer. This comprises intracomplex isomerization of the initial iminol-terminated (−C(OH)NH) form of the c n ′ species to the energetically more favorable, amide-terminated form (−C(O)–NH2) prior to Cα H• abstraction by the z m • species. The data indicate that the previously published H• transfer barriers are more energetically demanding than those of this multistep alternative. The rate-determining step is typically the intracomplex iminol isomerization, consistent with the substantial energetic favorability of the amide form of the c n species. The barriers to H• transfer still rise steeply as a function of the charge state. In agreement with experiment, evidence for product separation without H• transfer at a higher charge state is also provided.
