Changes In Fragmentation Patterns Research Articles

Conformational Characterization of Peptides and Proteins by 193 nm Ultraviolet Photodissociation in the Collision Cell of a Trapped Ion Mobility Spectrometry-Time-of-Flight Mass Spectrometer.

Ultraviolet photodissociation (UVPD) has been shown to be a versatile ion activation strategy for the characterization of peptides and intact proteins among other classes of biological molecules. Combining the high-performance mass spectrometry (MS/MS) capabilities of UVPD with the high-resolution separation of trapped ion mobility spectrometry (TIMS) presents an opportunity for enhanced structural elucidation of biological molecules. In the present work, we integrate a 193 nm excimer laser in a TIMS-time-of-flight (TIMS-TOF) mass spectrometer for UVPD in the collision cell and use it for the analysis of several mass-mobility-selected species of ubiquitin and myoglobin. The resultant data displayed differences in fragmentation that could be correlated with changes in protein conformation. Additionally, this mobility-resolved UVPD strategy was applied to collision-induced unfolded ions of ubiquitin to follow changes in fragmentation patterns relating to the extent of protein unfolding. This platform and methodology offer new opportunities for exploring how conformational variations are manifested in the fragmentation patterns of gas-phase ions.

Electron scattering with ethane adsorbed on rare gas multilayers: Hole transfer, coulomb decay, and ion dissociation.

Positive ion desorption following electron impact dissociative ionization of ethane adsorbed on Ar, Kr, and Xe multilayers has been studied as a function of incident electron energy from threshold to 100eV. Based on the dependence of ion yields on the identity of the rare gas, it is likely that the majority of ethane molecules undergo indirect ionization following hole transfer from the ionized underlying rare gas. This has also been corroborated by density of states calculations showing the energetic alignment of the outer valence states of ethane and the condensed rare gas ionization energies. Due to the near-resonant nature of charge transfer for single-hole states, the ethane molecular ion is excited to different final ionic states on different rare gases, which leads to differences in ion desorption yields and branching ratios. The quantitative yields increase with increasing ionization energy gap between the rare gas and ethane, in the order Ar > Kr > Xe. The large increase in yields from 25eV onwards for all rare gases is likely due to the formation and decay of two-hole states on neighboring rare gas and ethane molecules due to interatomic and intermolecular Coulomb decay (ICD) and not electron transfer mediated decay (ETMD). The ICD and ETMD pathways become accessible when the incoming electron has sufficient energy to excite the inner valence ns level of the rare gas to a Rydberg state or ionize it. The experimental findings are supported by calculations of thresholds, density of states for the final configurations of these processes, and coupling strengths for hole transfer between ethane and rare gases. The fragment ion branching ratios vary with energy from threshold to about 35eV, showing the fragmentation pattern changes with the mode of hole transfer and availability of excess energy. Sigma C-C bonds are more likely to break than C-H bonds in the mid-20eV range, and this effect is most pronounced for Xe, followed by Kr, and then Ar.

Coulomb Fission in Multiply-Charged Ammonia Clusters: Accurate Measurements of the Rayleigh Instability Limit from Fragmentation Patterns

A series of experiments have been undertaken on the fragmentation of multiply charged ammonia clusters, (NH3) nz+, where z ≤ 8 and n ≤ 850, to establish Rayleigh instability limits, whereby clusters at certain critical sizes become unstable due to Coulomb repulsion between the resident charges. Experimental results on size-selected clusters are found to be in excellent agreement with theoretical predictions of Rayleigh instability limits at all values of the charge. Electrostatic theory has been used to help identify fragmentation patterns on the assumption that the clusters separate into two dielectric spheres, and the predicted Coulomb repulsion energies used to establish pathways and the sizes of cluster fragments. The results show that fragmentation is very asymmetric in terms of both the numbers of molecules involved and the amount of charge each fragment accommodates. For clusters carrying a charge ≤+4, the results show that fragmentation proceeds via the loss of small, singly charged clusters. When clusters carry a charge of +5 or more, the experimental observations suggest a marked switch in behavior. Although the laboratory measurements equate to fragmentation via the loss of a large dication cluster, electrostatic theory supports an interpretation that involves the sequential loss of two smaller, singly charged clusters possibly accompanied by the extensive evaporation of neutral molecules. It is suggested that this change in fragmentation pattern is driven by the channelling of Coulomb repulsion energy into intermolecular modes within these larger clusters. Overall, the results appear to support the ion evaporation model that is frequently used to interpret electrospray experiments.

In-tube collision-induced dissociation for selected ion flow-drift tube mass spectrometry, SIFDT-MS: a case study of NO(+) reactions with isomeric monoterpenes.

Soft chemical ionisation techniques including selected ion flow tube mass spectrometry, SIFT-MS, and proton transfer reaction mass spectrometry, PTR-MS, cannot currently quantify individual isomers present simultaneously in samples, a notable example being atmospheric monoterpenes. A possible solution lies in integrating in-tube collision-induced dissociation, CID, into a selected ion flow-drift tube mass spectrometry, SIFDT-MS, instrument. In-tube CID was implemented by applying electrostatic potential difference between the resistive glass flow-drift tube downstream end and the nose cone of a quadrupole mass spectrometer. The resulting inhomogeneous electric field accelerates the product ions along the last 1mm before the nose cone and causes their dissociation in collisions with molecules of the buffer gas (4% air, 96% helium, 2mbar). Mass spectra of the product ions of NO(+) reactions with 3-carene, β-pinene, (S)-limonene and their mixture were obtained for variable potential difference. Potential difference up to 47.7V resulted in dramatic changes in the mass spectra due to fragmentation of the monoterpene radical molecular cations. The main observed fragments correspond to logical losses from different isomeric structures. Fragmentation increases with the potential difference and can be interpreted as single collision dissociation on air molecules at centre-of-mass energies of several eV. Combination of fragmentation patterns at different CID enables distinction of isomers in the mixture on the basis of pseudoinversion. In-tube CID represents a simple and low-cost extension to SIFDT-MS that allows real-time identification of isomeric products of ion-molecule reactions on the basis of their structural differences and corresponding changes in fragmentation patterns with CID energy without significantly changing the net reaction time important for absolute quantification. Copyright © 2016 John Wiley & Sons, Ltd.

Photo-fragmentation spectroscopy of benzylium and 1-phenylethyl cations

The electronic spectra of cold benzylium (C6H5-CH2 (+)) and 1-phenylethyl (C6H5-CH-CH3 (+)) cations have been recorded via photofragment spectroscopy. Benzylium and 1-phenylethyl cations produced from electrosprayed benzylamine and phenylethylamine solutions, respectively, were stored in a cryogenically cooled quadrupole ion trap and photodissociated by an OPO laser, scanned in parts of the UV and visible regions (600-225 nm). The electronic states and active vibrational modes of the benzylium and 1-phenylethyl cations as well as those of their tropylium or methyl tropylium isomers have been calculated with ab initio methods for comparison with the spectra observed. Sharp vibrational progressions are observed in the visible region while the absorption features are much broader in the UV. The visible spectrum of the benzylium cation is similar to that obtained in an argon tagging experiment [V. Dryza, N. Chalyavi, J. A. Sanelli, and E. J. Bieske, J. Chem. Phys. 137, 204304 (2012)], with an additional splitting assigned to Fermi resonances. The visible spectrum of the 1-phenylethyl cation also shows vibrational progressions. For both cations, the second electronic transition is observed in the UV, around 33,000 cm(-1) (4.1 eV) and shows a broadened vibrational progression. In both cases the S2 optimized geometry is non-planar. The third electronic transition observed around 40,000 cm(-1) (5.0 eV) is even broader with no apparent vibrational structures, which is indicative of either a fast non-radiative process or a very large change in geometry between the excited and the ground states. The oscillator strengths calculated for tropylium and methyl tropylium are weak. Therefore, these isomeric structures are most likely not responsible for these absorption features. Finally, the fragmentation pattern changes in the second and third electronic states: C2H2 loss becomes predominant at higher excitation energies, for both cations.

Temporal Change in Fragmentation in China’s Primary Forest Ecoregions

Forests are of interest from a wide range of perspectives simply because they serve many purposes, including timber products, watershed protection, wildlife habitat, carbon sequestration, recreational opportunities and aesthetic values. However, degradation or changes in forest ecosystem function and condition arise from changes in forest loss and fragmentation. In this study, based on the 1995 and 2005 land use/cover data for China, mathematical morphology coupled with the percolation theory was adopted to temporally assess changes in forest fragmentation patterns in 36 forest ecosystems of China through classifying each forest pixel into one of the six fragmentation components (interior, perforated, patch, edge, transitional and undetermined) by using the sliding window analysis technique to establish spatially explicit forest fragmentation maps. Additionally, landscape indices were also involved in the assessment of forest fragmentation status and trends. Results revealed that an accelerated fragmentation was observed in most forest ecoregions, especially in Daurian forest stepp, Hainan Island monsoon rain forests, and Northern Indochina subtropical forests with a sharp change in fragmentation patterns. The increased fragmentation was evidenced by a decreasing share of interior forest and an increasing trend of area share for perforated forest, patch forest and edge forest. In addition, derivations of geospatial indices from another three selected typical forest ecoregions also further confirmed the accelerated fragmentation. The increased fragmentation in most forest ecoregions of China was primarily driven by anthropogenic disturbances, including illegal logging, agricultural encroachment, infrastructure construction. Additionally, forest fragmentation maps provided valuable insights and implications regarding the development of land use strategies, habitat planning for rare and endangered species, and sustainable forest management. By utilizing the changes in fragmentation maps, such as the variation in location of the interior and perforated components, human can make effective risk assessments and crucial targets for protection and remediation.

Ion‐Induced Fragmentation of Amino Acids: Effect of the Environment

In general, radiation-induced fragmentation of small amino acids is governed by the cleavage of the C-C(α) bond. We present results obtained with 300 keV Xe(20+) ions that allow molecules (glycine and valine) to be ionised at large distances without appreciable energy transfer. Also in the present case, the C-C(α) bond turns out to be the weakest link and hence its scission is the dominant fragmentation channel. Intact ionised molecules are observed with very low intensities. When the molecules are embedded in a cluster of amino acids, a protective effect of the environment is observed. The fragmentation pattern changes: the C-C(α) bond becomes more protected and stable amino acid cations are observed as fragments of the molecular clusters. Evidently, the molecular cluster acts as a "buffer" for the excess energy, capable of rapidly redistributing excess energy and charge.

Fission processes following core level excitation in closo ‐1,2‐orthocarborane

AbstractTime‐of‐flight mass analysis with multi‐stop coincidence detection was used to study the multi‐cation ionic fragmentation of the closo carborane cage molecule closo ‐1,2‐orthocarborane (C2B10H12) following inner‐shell excitation in or above the B 1s regime. Electron ion coincidence spectra reveal the cationic products which are formed after core level excitation. Distinct changes in fragmentation pattern are observed as a function of excitation energy. Photoelectron–photoion–photoion coincidence (PEPIPICO) spectroscopy was used to study the dominant fission routes in the core level excitation regime. Series of ion pairs are identified, where asymmetric fission dominates, leading to ion pairs of different mass. Suitable fission and fragmentation mechanisms are discussed. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Characterizing the forest fragmentation of Canada’s national parks

Characterizing the amount and configuration of forests can provide insights into habitat quality, biodiversity, and land use. The establishment of protected areas can be a mechanism for maintaining large, contiguous areas of forests, and the loss and fragmentation of forest habitat is a potential threat to Canada's national park system. Using the Earth Observation for Sustainable Development of Forests (EOSD) land cover product (EOSD LC 2000), we characterize the circa 2000 forest patterns in 26 of Canada's national parks and compare these to forest patterns in the ecological units surrounding these parks, referred to as the greater park ecosystem (GPE). Five landscape pattern metrics were analyzed: number of forest patches, mean forest patch size (hectare), standard deviation of forest patch size (hectare), mean forest patch perimeter-to-area ratio (meters per hectare), and edge density of forest patches (meters per hectare). An assumption is often made that forests within park boundaries are less fragmented than the surrounding GPE, as indicated by fewer forest patches, a larger mean forest patch size, less variability in forest patch size, a lower perimeter-to-area ratio, and lower forest edge density. Of the 26 national parks we analyzed, 58% had significantly fewer patches, 46% had a significantly larger mean forest patch size (23% were not significantly different), and 46% had a significantly smaller standard deviation of forest patch size (31% were not significantly different), relative to their GPEs. For forest patch perimeter-to-area ratio and forest edge density, equal proportions of parks had values that were significantly larger or smaller than their respective GPEs and no clear trend emerged. In summary, all the national parks we analyzed, with the exception of the Georgian Bay Islands, were found to be significantly different from their corresponding GPE for at least one of the five metrics assessed, and 50% of the 26 parks were significantly different from their respective GPEs for all of the metrics assessed. The EOSD LC 2000 provides a heretofore unavailable dataset for characterizing broad trends in forest fragmentation in Canada's national parks and in their surrounding GPEs. The interpretation of forest fragmentation metrics must be guided by the underlying land cover context, as many forested ecosystems in Canada are naturally fragmented due to wetlands and topography. Furthermore, interpretation must also consider the management context, as some parks are designed to preserve fragmented habitats. An analysis of forest pattern such as that described herein provides a baseline, from which changes in fragmentation patterns over time could be monitored, enabled by earth observation data.

Wavelength-Dependent Photofragmentation of a Mixed-Ligand Cyclometalated Platinum(II) Coordination Compound in a Molecular Beam

The photofragmentation of (3-Me-4',6'-dfppy)Pt(dpm) (dfppy = difluorophenylpyridinato; dpm = dipivaloylmethyl or 2,2,6,6,-tetramethyl-3,5-heptanedionato- O, O) in a molecular beam is reported. Time-of-flight mass spectra (TOF-MS) and resonance-enhanced multiphoton ionization (REMPI) data are presented and discussed. The dissociation patterns are strongly wavelength-dependent. With 355 nm excitation, the heaviest mass platinum-containing fragments are Pt(+) and diatomic PtC(+). The formation of PtC(+) is the result of an intramolecular rearrangement on the ligand. During irradiation with 410-500 nm light, the fragmentation pattern changes such that the parent ion and platinum-containing fragments of the parent are formed in abundant yield. The (3-Me-4',6'-dfppy) ligand remains intact and coordinated to platinum, but coordinated (dpm) successively breaks apart. A spin-forbidden charge-transfer absorption band centered at around 460 nm plays an important role in the gas-phase photoexcitation of the parent molecule; it is observed in the REMPI spectrum of the parent ion.

Rydberg Matter clusters of hydrogen [formula omitted] with well-defined kinetic energy release observed by neutral time-of-flight

Neutral Rydberg Matter clusters of hydrogen ( H 2) N ∗ are studied using laser fragmentation neutral time-of-flight measurements outside a K impregnated iron oxide emitter in ultrahigh vacuum. A ns pulsed dye laser beam passing in front of the emitter releases the clusters by Coulomb explosions in the Rydberg Matter cloud surrounding the emitter. Well-resolved cluster peaks are observed, and the kinetic temperature of the clusters is low and well described by T/ N, where T is the emitter temperature and N is the number of H 2 molecules in the cluster. The clusters are neutral as verified by applying a negative voltage of a few V to the emitter, with no change in the flight times. The clusters receive a common excess kinetic energy of ⩽1 eV in the Coulomb explosions initiated by the laser pulse. The common excess kinetic energy shows that the clusters come from larger clusters or clouds with a large inertia. The sharp time-of-flight peaks show that the bonds in the Rydberg Matter broken by the laser are in just one specific quantum number state, n=3–7. The observed excess energy increases with laser intensity, and the fragmentation pattern changes simultaneously.

Inner-shell excitation and site specific fragmentation of poly(methylmethacrylate) thin film

Soft x-ray excitations in the 250–600 eV photon energy range on poly(methylmethacrylate) (PMMA) result in ionic fragmentation of the original polymer with the most intense ions corresponding to CH+3, H+, CH+2, CH+, CHO+, and COOCH+3. The photon energy dependence of ion desorption from thin films of PMMA was measured to investigate the primary steps in radiation induced decomposition following carbon and oxygen 1s electron excitations using monochromatic pulsed-synchrotron radiation. It was clearly found that the decomposition depends on the nature of the electronic states created in the excited species. The fragmentation pattern changes depending on the transitions of the 1s electron to a Rydberg orbital, an unoccupied molecular orbital or the ionization continuum. Moreover, the fragmentation occurs specifically around the site of the atom where the optical excitation takes place. Excitations from carbon and oxygen 1s to σ* states seem to be specially efficient for ion production as observed in the case of CH+3, CH+2, and CH+ at 288.7 and 535.6 eV, and in the case of CHO+ at 539.3 eV.

Site-specific fragmentation following inner-core level excitation of Pb(CH 3) 4 in the vapor phase

Ionic fragmentation following inner-shell (Pb 5p and 4f, C 1 s) excitation of Pb (CH 3) 4 has been studied in the vapor phase by use of synchrotron radiation and time-of-flight mass spectrometry. The C 1 s ionization is followed by KVV Auger process, and the fragmentation proceeds by way of the doubly charged parent ion. The Pb 5p or 4f ionization is followed by a cascade of Auger events, and the fragmentation proceeds by way of the triply or higher multiply charged parent ions. The fragmentation pattern changes significantly depending on the site of the core electrons excited (Pb or C).

Site-Specific Fragmentation of Small Molecules Following Soft-X-Ray Excitation.

Soft-x-ray excitation involving C $1s$ electrons in CO and acetone, ${(\mathrm{C}{\mathrm{H}}_{3})}_{2}$CO, is found to result in ionic fragmentation of the original molecule. The fragmentation pattern changes whether the C $1s$ electron gets ionized or excited into a Rydberg-line orbital or into an antibonding ${\ensuremath{\pi}}^{*}$ molecular orbital. Moreover, the fragmentation occurs specifically around the site of the carbon atom where the optical excitation takes place. Based on these observations one might consider the use of tunable soft x rays to stimulate chemical reactions or to selectively break large organic molecules.

Site-Specific Fragmentation of Small Molecules Following Soft-X-Ray Excitation

Soft-x-ray excitation involving C $1s$ electrons in CO and acetone, ${(\mathrm{C}{\mathrm{H}}_{3})}_{2}$CO, is found to result in ionic fragmentation of the original molecule. The fragmentation pattern changes whether the C $1s$ electron gets ionized or excited into a Rydberg-line orbital or into an antibonding ${\ensuremath{\pi}}^{*}$ molecular orbital. Moreover, the fragmentation occurs specifically around the site of the carbon atom where the optical excitation takes place. Based on these observations one might consider the use of tunable soft x rays to stimulate chemical reactions or to selectively break large organic molecules.