Correction: UV and VUV-induced fragmentation of tin-oxo cage ions.

Correction for 'UV and VUV-induced fragmentation of tin-oxo cage ions' by Jarich Haitjema et al., Phys. Chem. Chem. Phys., 2021, 23, 20909-20918, https://doi.org/10.1039/D1CP03148A.

Peptide Bond Formation in the Protonated Serine Dimer Following Vacuum UV Photon-Induced Excitation.

Possible routes for intra-cluster bond formation (ICBF) in protonated serine dimers have been studied. We found no evidence of ICBF following low energy collision-induced dissociation (in correspondence with previous works), however, we do observe clear evidence for ICBF following photon absorption in the 4.6-14 eV range. Moreover, the comparison of photon-induced dissociation measurements of the protonated serine dimer to those of a protonated serine dipeptide provides evidence that ICBF, in this case, involves peptide bond formation (PBF). The experimental results are supported by ab initio molecular dynamics and exploration of several excited state potential energy surfaces, unraveling a pathway for PBF following photon absorption. The combination of experiments and theory provides insight into the PBF mechanisms in clusters of amino acids, and reveals the importance of electronic excited states reached upon UV/VUV light excitation.

UV-VUV Photofragmentation Spectroscopy of Isolated Neutral Fragile Macromolecules: A Proof-of-Principle Based on a Deprotonated Vancomycin-Peptide Noncovalent Complex.

The gas phase offers the possibility to analyze organic molecules by ultraviolet-vacuum ultraviolet (UV-VUV) spectroscopy without any solvent effect or limitation in terms of spectral range due to absorption by the solvent. Up to now, the size and chemical composition of neutral molecular systems under study have been limited by the use of vaporization methods based on thermal heating. Soft sources of gas-phase thermolabile molecular systems such as electrospray or matrix-assisted laser desorption ionization are appealing alternatives to heating-based techniques, but they lead to the production of ions. In such cases, UV-VUV action spectroscopy is then the method of choice to study the electronic structure and corresponding photodynamics of these gas-phase molecular ions. However, previous investigations have shown that the UV-VUV action spectrum of a given molecular ion depends on the charge state, which in many cases might be a caveat. Here, by means of synchrotron radiation coupled to mass spectrometry and through the test case of the glycopeptide antibiotic vancomycin noncovalently bound to a deprotonated small peptide, we show that the UV-VUV photofragmentation spectrum of neutral thermally fragile organic molecules can be obtained via charge-tagging action spectroscopy.

Mammal hyaluronidase activity on chondroitin sulfate and dermatan sulfate: Mass spectrometry analysis of oligosaccharide products.

Mammalian hyaluronidases are endo-N-acetyl-D-hexosaminidases involved in the catabolism of hyaluronic acid (HA) but their role in the catabolism of chondroitin sulfate (CS) is also examined. HA and CS are glycosaminoglycans implicated in several physiological and pathological processes, and understanding their metabolism is of significant importance. Data have been previously reported on the degradation of CS under the action of hyaluronidase, yet a detailed structural investigation of CS depolymerization products remains necessary to improve our knowledge of the CS depolymerizing activity of hyaluronidase. For that purpose, the fine structural characterization of CS oligosaccharides formed upon the enzymatic depolymerization of various CS subtypes by hyaluronidase has been carried out by high-resolution Orbitrap mass spectrometry (MS) and extreme UV (XUV) photodissociation tandem MS. The exact mass measurements show the formation of wide size range of even oligosaccharides upon digestion of CS-A and CS-C comprising hexa- and octa-saccharides among the main digestion products, as well as formation of small quantities of odd-numbered oligosaccharides, while no hyaluronidase activity was detected on CS-B. In addition, slight differences have been observed in the distribution of oligosaccharides in the digestion mixture of CS-A and CS-C, the contribution of longer oligosaccharides being significantly higher for CS-C. The sequence of CS oligosaccharide products determined XUV photodissociation experiments verifies the selective ß(1 â†’ 4) glycosidic bond cleavage catalyzed by mammal hyaluronidase. The ability of the mammal hyaluronidase to produce hexa- and higher oligosaccharides supports its role in the catabolism of CS anchored to membrane proteoglycans and in extra-cellular matrix.

UV and VUV-induced fragmentation of tin-oxo cage ions.

Photoresist materials are being optimized for the recently introduced Extreme Ultraviolet (EUV) photolithographic technology. Organometallic compounds are potential candidates for replacing the ubiquitous polymer-based chemically amplified resists. Tin (Sn) has a particularly large absorption cross section for EUV light (13.5 nm, 92 eV), which could lead to a lower required EUV dose for achieving the desired solubility change (improved sensitivity). However, the fundamental interaction between organometallic materials and higher energy photons is poorly understood. In this work, we exposed n-butyltin-oxo cage dications (M2+) in the gas phase to photons in the energy range 4-35 eV to explore their fundamental photoreactivity. Photoproducts were detected using mass spectrometry. Homolytic cleavage of tin-carbon bonds was observed for all photon energies above the onset of electronic absorption at ∼5 eV (∼250 nm), leading to photoproducts which have lost one or more of the attached butyl groups (Bu). Above 12 eV (<103 nm), dissociative photoionization occurred for the dication (M2+), competing with the neutral loss channels. The photoionization threshold is lowered by approximately 2 eV when one counterion (triflate, OTf- or tosylate, OTs-) is attached to the tin-oxo cage (MOTf+ and MOTs+). This threshold is expected to be even lower if each tin-oxo cage is attached to two counterions, as is the case in a solid film of tin-oxo cages. Addition of counterions also affected the fragmentation pathways; photoexcitation of (MX)+ (X = counterion, OTf or OTs) always led to formation of (MX-2Bu)+ rather than (MX-Bu)+. MOTs+ was much more reactive than MOTf+ in terms of reaction products per absorbed photon. A possible explanation for this is proposed, which involves the counterion reacting with the initially formed tin-based radical.

Synchrotron UV photoactivation of trapped sodiated ions produced from poly(ethylene glycol) by electrospray ionization.

RATIONALE: By taking advantage of the gas-phase decompositions of polymer ions, tandem mass spectrometry of polymers allows us to obtain more accurate structural information than from a simple mass measurement. Applied to a model polymer, the goal of this work was to evaluate the performances of an activation technique based on ultraviolet (UV) irradiation, as an alternative to conventional collisional activation. METHODS: Sodiated poly(ethylene glycol) produced by electrospray ionization was isolated in a linear ion trap, then submitted to synchrotron UV irradiation over a range of wavelengths (52 to 248 nm). Fragmentation pathways resulting from UV photoactivation were investigated. The proposed mechanisms take into account: (i) the comparison with collision-induced dissociation (CID) product ions, (ii) the effect of wavelength-tunable UV activation, and (iii) deuterium-labeling and various other complementary experiments. For the highest molecular weight compounds, ion mobility spectrometry was used before UV photoactivation. RESULTS: Synchrotron UV irradiation can induce dissociation of poly(ethylene glycol) sodiated ions without the requirement of the presence of a specific chromophore, if the photon energy is above 10 eV. UV photoactivation of poly(ethylene glycol) ions can yield fragmentations that differ from those in classical low-energy CID, especially from higher masses (>4000 g mol-1 ). A successful coupling of UV photoactivation with ion mobility pre-filtering was presented. CONCLUSIONS: UV activation combined or not with pre-filtering ion mobility is a promising alternative approach for the structural characterization of polymers. UV synchrotron radiation with a tunable wavelength was a great opportunity to study the effect of the photon energy, and to probe the mechanisms of ion decomposition from poly(ethylene glycol).

Oxygen K-shell spectroscopy of isolated progressively solvated peptide.

Gas-phase near-edge X-ray-absorption fine structure (NEXAFS) action spectroscopy around the oxygen K-edge and mass spectrometry were employed to probe isolated substance P (SP) molecular ions, both bare and progressively solvated with 4 and 11 water molecules. Detailed mass spectra of bare and hydrated precursors are presented for the resonant photon energy of 532 eV that corresponds to O1s →π(amide)* core excitation, triggering resonant Auger decay and fragmentation from the ionized radical molecular system. The fragmentation pattern of doubly protonated SP hydrated with 4 water molecules clearly shows a series of abundant doubly charged backbone fragments, as well as triply charged precursor with small neutral losses, all preserving full water cluster. This is drastically different from the collisional induced dissociation of the hydrated peptide where the water loss is a dominant relaxation process. Moreover, the action NEXAFS obtained from several resolved small backbone fragments revealed increased fragmentation of hydrated SP relative to the bare one, due to a resonant O1s excitation of the attached water molecules. Such unexpected result inspires further experimental developments to investigate possible nonlocal energy transfer from the solvent to the biomolecules within the first solvation shell. The experiment is supported by molecular dynamics and DFT calculations to estimate the intensity of the resonant X-ray absorption of bare and hydrated SP around peptide and water O1s excitation region.

Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks - Influence of the DNA Sequence and Substrate.

DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF2 as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7-2.3×10-16  cm2 . The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.

Vacuum-UV induced DNA strand breaks - influence of the radiosensitizers 5-bromouracil and 8-bromoadenine.

Radiation therapy is a basic part of cancer treatment. To increase the DNA damage in carcinogenic cells and preserve healthy tissue at the same time, radiosensitizing molecules such as halogenated nucleobase analogs can be incorporated into the DNA during the cell reproduction cycle. In the present study 8.44 eV photon irradiation induced single strand breaks (SSB) in DNA sequences modified with the radiosensitizer 5-bromouracil (5BrU) and 8-bromoadenine (8BrA) are investigated. 5BrU was incorporated in the 13mer oligonucleotide flanked by different nucleobases. It was demonstrated that the highest SSB cross sections were reached, when cytosine and thymine were adjacent to 5BrU, whereas guanine as a neighboring nucleobase decreases the activity of 5BrU indicating that competing reaction mechanisms are active. This was further investigated with respect to the distance of guanine to 5BrU separated by an increasing number of adenine nucleotides. It was observed that the SSB cross sections were decreasing with an increasing number of adenine spacers between guanine and 5BrU until the SSB cross sections almost reached the level of a non-modified DNA sequence, which demonstrates the high sequence dependence of the sensitizing effect of 5BrU. 8BrA was incorporated in a 13mer oligonucleotide as well and the strand breaks were quantified upon 8.44 eV photon irradiation in direct comparison to a non-modified DNA sequence of the same composition. No clear enhancement of the SSB yield of the modified in comparison to the non-modified DNA sequence could be observed. Additionally, secondary electrons with a maximum energy of 3.6 eV were generated when using Si as a substrate giving rise to further DNA damage. A clear enhancement in the SSB yield can be ascertained, but to the same degree for both the non-modified DNA sequence and the DNA sequence modified with 8BrA.

State-Dependent Fragmentation of Protonated Uracil and Uridine.

Action spectroscopy using photon excitation in the VUV range (photon energy 4.5-9 eV) was performed on protonated uracil (UraH+) and uridine (UrdH+). The precursor ions with m/ z 113 and m/ z 245, respectively, were produced by an electrospray ionization source and accumulated inside a quadrupole ion trap mass spectrometer. After irradiation with tunable synchrotron radiation, product ion mass spectra were obtained. Fragment yields as a function of excitation energy show several maxima that can be attributed to the photoexcitation into different electronic states. For uracil, vertically excited states were calculated using the equation-of-motion coupled cluster approach and compared to the observed maxima. This allows to establish correlations between electronic states and the resulting fragment masses and can thus help to disentangle the complex de-excitation and fragmentation pathways of nucleic acid building blocks. Photofragmentation of the nucleoside uridine shows a significantly lower variety of fragments, indicating stabilization of the nucleobase by the attached sugar.

Extreme Ultraviolet Radiation: A Means of Ion Activation for Tandem Mass Spectrometry.

Tandem mass spectrometry has long been established as a corner stone of analytical and structural chemistry. Fast radical-directed dissociation, produced by electron-transfer and electron-capture dissociation (ETD and ECD) has been shown to provide important complementary information to collision-induced dissociation (CID). We report the first application of extreme-ultraviolet (XUV) lamps to tandem mass spectrometry. These discharge lamps are versatile, robust, and low-cost sources of energetic photons (40-80 nm). The coupling of the discharge lamp with a Waters Synapt G2-Si Q-ToF mass spectrometer is achieved through a specific trapping scheme in the TriWave region of the instrument, allowing efficient irradiation of the precursor ions. Rich radical-directed dissociation was produced for a number of model compounds, providing unique, complementary information to existing dissociation techniques.

Spectroscopy and Photodissociation of the Perfluorooctanoate Anion.

Perfluorocarbons, a class of fully fluorinated compounds, are highly persistent and toxic pollutants that are receiving increasing attention due to their widespread environmental distribution. In this study, attention was focused on one compound in particular, namely, perfluorooctanoic acid (PFOA). The first investigation of the UV/VUV photochemistry of the PFOA anion in the gas phase by action spectroscopy of selected ions is reported. Two main relaxation channels were identified: photodissociation and photodetachment. Absolute cross sections for the individual observed processes were measured. DFT calculations and natural transition orbital analysis were carried out to help in the interpretation of the experimental results.

MS/MS-Guided Isolation of Clarinoside, a New Anti-Inflammatory Pentalogin Derivative.

Re-investigation of the chemical composition of the annual plant Mitracarpus scaber Zucc. led to the identification of clarinoside, a new pentalogin derivative containing a rare quinovose moiety, and the known compound harounoside. While the planar structure was fully determined using tandem mass spectrometry (MS) and quantum mechanics (QM) calculations, the tridimensional structure was unravelled after isolation and NMR analysis. The absolute configuration was assigned by comparison of experimental and theoretical synchrotron radiation circular dichroism spectra. Both compounds were tested for anti-inflammatory activity, and compound 1 showed the ability to inhibit the production of interleukin-8 (Il-8) with an IC 50 value of 9.17 µ M.

Investigation of secondary structure evolution of micellar casein powder upon aging by FTIR and SRCD: consequences on solubility.

BACKGROUND: Synchrotron radiation circular dichroism (SRCD) and Fourier transform infrared (FTIR) spectroscopy were used to examine the conformation evolution of micellar casein (MC) powder during storage and to determine whether the spectral changes could be related to their solubility evolution. RESULTS: A loss in intensity of SRCD spectra as a function of storage time has been observed. Quantification of secondary structures revealed losses of α-helix content during storage. Moreover, a redshift of the amide I band in the FTIR spectrum was demonstrated during the storage and was interpreted as a rearrangement of the secondary structure of the protein, which is in line with the SRCD results. The qualitative results obtained by FTIR clearly support the quantitative evolution of the secondary structure obtained by the analysis of SRCD spectra. Principal component analysis (PCA) of FTIR spectra permits a good separation of samples according to the storage time. PCA shows that the evolution of secondary structures and solubility loss are closely linked. CONCLUSION: With the quantitative data provided by SRCD spectra, it was established that, whatever the storage conditions, a unique curve exists between loss of α-helix content and loss in solubility, showing that loss of α-helix content is a marker of solubility loss for the MC powders studied. © 2017 Society of Chemical Industry.

Probing the solution structure of Factor H using hydroxyl radical protein footprinting and cross-linking.

The control protein Factor H (FH) is a crucial regulator of the innate immune complement system, where it is active on host cell membranes and in the fluid phase. Mutations impairing the binding capacity of FH lead to severe autoimmune diseases. Here, we studied the solution structure of full-length FH, in its free state and bound to the C3b complement protein. To do so, we used two powerful techniques, hydroxyl radical protein footprinting (HRPF) and chemical cross-linking coupled with mass spectrometry (MS), to probe the structural rearrangements and to identify protein interfaces. The footprint of C3b on the FH surface matches existing crystal structures of C3b complexed with the N- and C-terminal fragments of FH. In addition, we revealed the position of the central portion of FH in the protein complex. Moreover, cross-linking studies confirmed the involvement of the C-terminus in the dimerization of FH.

High-energy photon activation tandem mass spectrometry provides unprecedented insights into the structure of highly sulfated oligosaccharides extracted from macroalgal cell walls.

Extreme ultraviolet photon activation tandem mass spectrometry (MS) at 69 nm (18 eV) was used to characterize mixtures of oligo-porphyrans, a class of highly sulfated oligosaccharides. Porphyrans, hybrid polymers whose structures are far from known, continue to provide a challenge for analytical method development. Activation by 18 eV photons led to a rich fragmentation of the oligo-porphyrans, with many cross-ring and glycosidic cleavages. In contrast to multistage MSn strategies such as activated electron photodetachment dissociation, a single step of irradiation by energetic UV of multiply charged anions led to a complete fragmentation of the oligo-porphyrans. In both ionization modes, the sulfate groups were retained on the backbone, which allowed the pattern of these modifications along the porphyran backbone to be described in unprecedented detail. Many structures released by the enzymatic degradation of the porphyran were completely resolved, including isomers. This work extends the existing knowledge of the structure of porphyrans. In addition, it provides a new demonstration of the potential of activation by high-energy photons for the structural analysis of oligosaccharides, even in unseparated mixtures, with a particular focus on sulfated compounds.

Contribution of synchrotron radiation to photoactivation studies of biomolecular ions in the gas phase.

Photon activation of ions in the visible and ultraviolet range attracts a growing interest, partly for its promising applications in tandem mass spectrometry. However, this task is not trivial, as it requires notably high brilliance photon sources. Hence, most of the work in that field has been performed using lasers. Synchrotron radiation is a source continuously tunable over a wide photon energy range and which possesses the necessary characteristics for ion activation. This review focuses on the array of applications of synchrotron radiation in photon activation of ions ranging from near UV to soft X-rays.

Action spectroscopy of a protonated peptide in the ultraviolet range.

Action spectroscopy of protonated substance P, a model undecapeptide, has been probed from 5.2 eV to 20 eV. For photon energy above the ionization threshold measured at 10.3 ± 0.1 eV, the radical dication is observed along with side chain losses and abundant formation of all kinds of sequence ions. Below the photoionization threshold, the photoproducts involve side chain cleavages and backbone cleavages into a-, b-/y-, and c-sequence ions. Different electronic excited states appear to produce different fragment ions. Norrish type I and II reactions are proposed to account for some photoproducts. This study bridges the gap between laser activation and electron-induced dissociation of peptides. Moreover, our results report for the first time a comprehensive picture of the photochemical fragmentation of a gas phase peptide in a wide photon energy range.

Gas-phase VUV photoionisation and photofragmentation of the silver deuteride nanocluster [Ag10D8L6](2+) (L = bis(diphenylphosphino)methane). A joint experimental and theoretical study.

The bis(diphenylphosphino)methane (L = Ph2PCH2PPh2) ligated silver deuteride nanocluster dication, [Ag10D8L6](2+), has been synthesised in the condensed phase via the reaction of bis(diphenylphosphino)methane, silver nitrate and sodium borodeuteride in the methanol : chloroform (1 : 1) mixed solvent system. The photoionisation and photofragmentation of this mass-selected cluster were studied using a linear ion trap coupled to the DESIRS VUV beamline of the SOLEIL Synchrotron. At 15.5 eV the main ionic products observed are [Ag10D8L5](2+), [Ag10D8L4](2+), [Ag10D8L6](3+)˙, [Ag9D8L4](2+)˙, and [AgL2](+). The later two products arise from fragmentation of [Ag10D8L6](3+)˙. An analysis of the yields of these product ions as a function of the photon energy reveals the onset for the formation of [AgL2](+) and [Ag9D8L4](2+)˙ is around 2 eV higher than that for ionisation to produce [Ag10D8L5](3+)˙. The onset of ionisation energy of [Ag10D8L6](2+) was determined to be 9.3 ± 0.3 eV from a fit of the yield of the product ion, [Ag10D8L6](3+)˙, as a function of the VUV photon energy. DFT calculations at the RI-PBE/RECP-def2-SVP level of theory were carried out to search for a possible structure of the cluster and to estimate its vertical and adiabatic ionisation energies. The calculated lowest energy structure of the [Ag10D8L6](2+) nanocluster contains a symmetrical bicapped square antiprism as a silver core in which hydrides are located as a mix of triangular faces and edges. Four of the bisphosphines bind to the edges of the cluster core as bidentate ligands, the remaining two bisphosphines bind via a single phosphorus donor atom to each of the apical silver atoms. The DFT calculated adiabatic ionisation energy for this structure is 8.54 eV, in satisfactory agreement with experiment.

Fold of an oleosin targeted to cellular oil bodies.

In cells, from bacteria to plants or mammals, lipids are stored in natural emulsions called oil bodies (OBs). This organelle is surrounded by a phospholipid monolayer which is thought to contain integral proteins involved in its stabilization. The insertion and fold of these proteins into the phospholipid monolayer are poorly understood. In seed OBs, the most abundant integral proteins are oleosins, which contain a 70-residue central hydrophobic domain. The secondary structure of solubilized oleosins varies greatly from mainly alpha helices to a predominantly beta sheets depending on the detergent used. To study the fold of integral membrane proteins inserted in a cellular OB environment, S3 protein, the major Arabidopsis thaliana seed oleosin, was targeted to Saccharomyces cerevisiae OBs. The diameter of purified yeast OBs harboring S3 or S3 fused with the Green Fluorescent Protein (GFP) was smaller and more homogeneous than plant OBs. Comparison of the secondary structure of S3 and S3-GFP was used to validate the structure of folded S3. Circular dichroism using synchrotron radiation indicated that S3 and S3-GFP in yeast OBs contain mainly beta secondary structures. While yeast OBs are chemically different to A. thaliana seed OBs, this approach allowed the secondary structure of S3 in OB particles to be determined for the first time.