Fragmentation Of Negative Ions Research Articles

<i>Ab initio</i> molecular dynamics study on dissociation process of 2-thiouracil and its tautomers under low-energy electron interactions

When biomolecules interact with high-energy particles and rays, they are directly ionized or dissociated, then a large number of low-energy electrons are formed as secondary particles. These low-energy electrons will attach to biomolecules, and trigger off the secondary dissociation, forming free radicals and ions with high reactivity, which can damage the structure and function of the biomolecule and cause irreversible radiation damage to the biomolecule. It is important to study the low-energy dissociative electron attachment (DEA) process of biomolecules for understanding radiation damage to biological organisms. Currently, the theoretical studies of DEA have mainly focused on the bound states of negative ions and the types of resonances in the dissociation process. The dissociation process is well described by quantum computational method, but the diversity and complexity of dissociation channels present in the dissociation process of 2-thiouracil molecule also pose a great computational challenge to these methods. In addition, the quantum computational methods are not ideal for dealing with the discrete states of chemical bonds and the problem of continuity coupling of electrons. The dissociation dynamics of biomolecules mainly results from ionization and electron attachment. <i>Ab initio</i> molecular dynamics simulation can reasonably describe these processes. In light of these considerations, <i>ab initio</i> molecular dynamics simulation is used in this work to study dynamic variation process in DEA. The low-energy electron dissociative attachment to 2-thiouracil in the gas phase is studied by using the Born-Oppenheimer molecular dynamics model combined with density functional theory. It is found that an important dehydrogenation phenomenon of 2-thiouracil and its tautomers occurs in the DEA process, and that the N—H and C—H bond are broken at specific locations. Due to the loss of hydrogen atoms at the N and C sites, the closed-shell dehydrogenated negative ion (TU-H)<sup>–</sup> forms, which is the most important negative ion fragments in the dissociation process. The potential energy curves, the bond dissociation energy and the electron affinity energy of the broken bond show that the N—H bond is the most likely to break, indicating the formation of the negative ion (TU-H)<sup>–</sup> mainly comes from the breaking of N—H bond. The theoretical calculations in this work are in good agreement with the available experimental results, indicating that the chosen calculation method is fully reliable. ​The BOMD simulations can not only dynamically recover the process of dissociative attachment of low-energy electrons to 2-thiouracil, but also more importantly provide an insight into the mechanisms of dehydrogenation and dissociation channels of 2-thiouracil molecules in DEA process.

Electron Capture Dissociation by Triclocarban Molecules

The formation and decay of molecular negative ions (MNIs) formed during resonant scattering of electrons by triclocarban molecules were studied by dissoiative electron attachment (DEA) spectroscopy. The most intense channel observed in the mass spectrum are MNIs formed at the thermal energy of trapped electrons with a lifetime relative to electron autodetachment of ~2800 μs. The experimental results were interpreted using CAM-B3LYP/6-311+G(d,p) calculations, which made it possible to reveal a number of important features of the geometry of molecular and fragment negative ions. Namely, the most stable geometry of MNIs is such that one of the chlorine atoms is coordinated with two hydrogen atoms of the structural element of urea. The charge on the chlorine atom is ~–0.7e–, which allows us to interpret this state as the result of the “roaming” of the chlorine atom in the MNI. According to calculations, the adiabatic electron affinity (EAa) of the triclocarban molecule is 1.66 eV. Evaluation of EAa in a simple Arrhenius approximation gives 1.2–1.4 eV. An analysis of the potential of the appearance of fragment ions with a C6H3Cl2NH2 structure made it possible to discover the noncovalent structure of these pseudo-MNIs, in which the chlorine atom is coordinated with two hydrogen atoms of the amino group.

Major benznidazole metabolites in patients treated for Chagas disease: Mass spectrometry-based identification, structural analysis and detoxification pathways

Benznidazole is the drug of choice for the treatment of Chagas disease, but its metabolism in humans is unclear. Here, we identified and characterized the major benznidazole metabolites and their biosynthetic mechanisms in humans by analyzing the ionic profiles of urine samples from patients and untreated donors through reversed-phase UHPLC-ESI-QTOF-MS and UHPLC-ESI-QqLIT-MS. A strategy for simultaneous detection and fragmentation of characteristic positive and negative ions was employed using information-dependent acquisitions (IDA). Selected precursor ions, neutral losses, and MS3 experiments complemented the study. A total of six phase-I and ten phase-II metabolites were identified and structurally characterized in urine of benznidazole-treated patients. Based on creatinine-corrected ion intensities, nitroreduction to amino-benznidazole (M1) and its subsequent N-glucuronidation to M5 were the main metabolic pathways, followed by imidazole-ring cleavage, oxidations, and cysteine conjugations. This extensive exploration of benznidazole metabolites revealed potentially toxic structures in the form of glucuronides and glutathione derivatives, which may be associated with recurrent treatment adverse events; this possibility warrants further exploration in future clinical trials. Incorporation of this knowledge of the benznidazole metabolic profile into clinical pharmacology trials could lead to improved treatments, facilitate the study of possible drug-drug interactions, and even mitigation of adverse drug reactions.

Plasmonic Hydroxyl Radical-Driven Epoxidation of Fatty Acid Double Bonds in Nanoseconds for On-Tissue Mass-Spectrometric Analysis and Bioimaging.

Lipids represent a large family of compounds with highly diverse structures that are involved in complex biological processes. A photocatalytic technique of on-tissue epoxidation of C=C double bonds has been developed for in situ mass spectrometric identification and spatial imaging of positional isomers of lipids. It is based on the plasmonic hot-electron transfer from irradiated gold nanowires to redox-active organic matrix compounds that undergo bond cleavages and generate hydroxyl radicals in nanoseconds. Intermediate radical anions and negative fragment ions have been unambiguously identified. Under the irradiation of a pulsed laser of the third harmonic of Nd3+:YAG (355 nm), the hydroxyl radical-driven epoxidation of unsaturated lipids with different numbers of C=C bonds can be completed in nanoseconds with high yields of up to 95%. Locations of C=C bonds were recognized with diagnostic fragment ions that were produced by either collision with an inert gas or auto-fragmentation resulting from the impact of energetic hot electrons and vibrational excitation. This technique has been applied to the analysis of breast cancer tissues of mice models without extensive sample processes. It was experimentally demonstrated that C=C bonds may be formed at different positions of not only regular mono- or poly-unsaturated fatty acids but also other odd-numbered long-chain fatty acids.

Further Analytical Studies on a Mercuri Thiol Adduct Isolated from a Human Prostate Cancer Cell Line (LNCaP)

Thiols play vital roles in cellular metabolism knowledge of which may be important in the design of future anticancer drugs. Previous work on the composition of the thiols present in human cancer cell lines has shown the presence of an unknown low molecular weight species, deemed to be a “Conthiol”, which could be important in this respect. This was prepared and isolated from a human prostate cancer cell line (LNCaP) in the form of an adduct of 2-mercuri-4-nitrophenol; it accounts for 56.5% of the total cellular thiols present in this cell line. Initial LC-MS analysis of this adduct had indicated that the possible molecular weight of the thiol was in the region of 467 daltons. In further analytical studies to identify the thiol, attempts were made to release it from the adduct by passage through a Thiopropyl Sepharose6B column. LC-MS analysis of the column eluate revealed two components yielding negative ion fragments of 427 m/z and 449 m/z. Only the former component contained thiol, indicating that a breakdown and/or possible rearrangement of the Conthiol had occurred. Further investigations of the column thiol eluate using ICP-MS analysis showed that the sulfur content agreed with the spectrophotometric analysis result (Ellman assay) and that the molecule did not contain phosphate. Amino acid analyses of the eluate were negative. In an attempt to prevent the breakdown of the thiol released by the Thiopropyl Sepharose 6B column, the adduct was treated with 5% v/v bromine water prior to applying to the column. In this instance the thiol containing eluate obtained from the column was treated with an equimolar quantity of mercuric chloride forming a fresh adduct, RS-Hg-SR. LC-MS analysis of this mercurial adduct detected a negative ion fragment of 782 m/z which on further ionization gave a ladder like pattern showing loss of mass units of 58 in each rung. This would seem to suggest the presence of a repeat polymer like structure containing 5 monomers, which, plus the thiol atom, gives a possible formula weight of 322; probably revealing only a part of the unknown Conthiol molecule whose properties and formula weight do not correlate with any known cellular thiol. Further analysis of the thiol released from the adduct on the Thiopropyl Sepharose 6B column by Infra-red (FTIR) provided little information except to confirm the presence of the thiol group and C=O stretch bands together with the possibility of a lactam ring at 1651 and 1634 cm·s&#451.

Identification of N-glycans with GalNAc-containing antennae from recombinant HIV trimers by ion mobility and negative ion fragmentation

Negative ion collision-induced dissociation (CID) of underivatized N-glycans has proved to be a simple, yet powerful method for their structural determination. Recently, we have identified a series of such structures with GalNAc rather than the more common galactose capping the antennae of hybrid and complex glycans. As part of a series of publications describing the negative ion fragmentation of different types of N-glycan, this paper describes their CID spectra and estimated nitrogen cross sections recorded by travelling wave ion mobility mass spectrometry (TWIMS). Most of the glycans were derived from the recombinant glycoproteins gp120 and gp41 from the human immunodeficiency virus (HIV), recombinantly derived from human embryonic kidney (HEK 293T) cells. Twenty-six GalNAc-capped hybrid and complex N-glycans were identified by a combination of TWIMS, negative ion CID, and exoglycosidase digestions. They were present as the neutral glycans and their sulfated and α2→3-linked sialylated analogues. Overall, negative ion fragmentation of glycans generates fingerprints that reveal their structural identity.

Time-of-flight secondary ion mass spectrometry fragment regularity in gallium-doped zinc oxide thin films

Time-of-flight secondary ion mass spectrometry fragment analysis remains a challenging task. The fragment appearance regularity (FAR) rule is particularly useful for two-element compounds such as ZnO. Ion fragments appearing in the form of ZnxOy obey the rule 2x ge 2y + 1 in the positive secondary ion spectrum and 2x le 2y + 1 in the negative spectrum where the valence of Zn is + 2 and that of O is − 2. Fragment analysis in gallium-doped ZnO (GZO) films can give insights into the bonding of the elements in this important semiconductor. Fragment analysis of 1 and 7 wt% GZO films shows that only the negative ion fragments obey the FAR rule where ZnO‒, 66ZnO‒, 68ZnO‒ and ZnO2‒ ion fragments appear. In the positive polarity, subdued peaks from out-of-the-rule ZnO+, 66ZnO+ and 68ZnO+ ion fragments are observed. The Ga ion peaks are present in both the positive and negative spectra. The secondary ion spectra of undoped ZnO also shows consistency with the FAR rule. This implies that Ga doping even in amounts that exceed the ZnO lattice limit of solubility does not affect the compliance with the FAR rule.

Thymidine and stavudine molecules in reactions with low-energy electrons

The negative ion formation and fragmentation processes in thymidine and stavudine were studied by means of resonant electron capture mass spectrometry in the electron energy range 0–14 eV. Stavudine is a nucleoside analog of thymidine, that differs from the latter by the presence of double bond in the deoxyribose moiety. In the energy range below 5 eV transient negative ions have been found to arise via shape resonances resulting in electron attachment into the empty π*-orbitals. The main fragmentation channels for molecular ions are the H-atom loss and N-glycosidic bond cleavage between sugar and a nucleobase moieties. The dissociative electron attachment cross sections for the fragment negative ions were measured. The structures for some observed anions and neutral counterparts were suggested basing on the thermochemical approach for dissociative reactions energy balance under the support of quantum chemical calculations. The processes of ion formation in thymidine were found to be similar to those revealed previously for deoxyuridine nucleoside. In contrast, very strong dissociative channel was found for stavudine yielding [M–R]– ions (where R is a sugar moiety) in the energy range <3 eV. The efficient fragmentation found for stavudine in the low energy electron attachment reactions may have implications for the design of nucleoside radiosensitizers for cancer therapy.

Electron-Transfer-Induced Side-Chain Cleavage in Tryptophan Facilitated through Potassium-Induced Transition-State Stabilization in the Gas Phase.

Fragmentation of transient negative ions of tryptophan molecules formed through electron transfer in collisions with potassium atoms is presented for the first time in the laboratory collision energy range of 20 up to 100 eV. In the unimolecular decomposition process, the dominating side-chain fragmentation channel is assigned to the dehydrogenated indoline anion, in contrast to dissociative electron attachment of free low-energy electrons to tryptophan. The role of the collision complex formed by the potassium cation and tryptophan negative ion in the electron transfer process is significant for the mechanisms that operate at lower collision energies. At those collision times, on the order of a few tens of fs, the collision complex may not only influence the lifetime of the anion but also stabilize specific transition states and thus alter the fragmentation patterns considerably. DFT calculations, at the BHandHLYP/6-311++G(3df,2pd) level of theory, are used to explore potential reaction pathways and the evolvement of the charge distribution along those.

Negative ion formation and fragmentation upon dissociative electron attachment to the nicotinamide molecule.

Nicotinamide (C6H6N2O) is a biologically relevant molecule. This compound has several important roles related to the anabolic and metabolic processes that take place in living organisms. It is also used as a radiosensitizer in tumor therapy. As a result of the interaction of high-energy radiation with matter, low-energy electrons are also released, which can also interact with other molecules, forming several types of ions. In the present investigation, dissociative electron attachment to C6H6N2O has been studied in a crossed electron-molecular beams experiment in the electron energy range of about 0–15 eV. In the experiment, six anionic species were detected: C6H5N2O−, C5H4N−, NCO−, O−/NH2−, and CN−, with NCO− being the most prominent anion. We also provide detailed computational results regarding the energetic thresholds and pathways of the respective dissociative electron attachment (DEA) channels. The experimental results are compared with the theoretical ones and on this basis, the possible DEA reactions for the formation of anions at a given resonance energy were assigned as well as the generation of neutrals fragments such as pyridine and its several derivatives and radicals are predicted. The pyridine ring seems to stay intact during the DEA process.

Determination of Electron Affinity on the Base of Experimentally Measured Lifetime of Negative Molecular Ions of Coumarin Derivatives

Resonance attachment of low-energy (0–15 eV) electrons to molecules of 4.7- and 6.7-dihydroxycoumarin was investigated by means of negative ion mass spectrometry. These natural compounds possess biological activity associated with antioxidant and bactericidal properties. The most probable structures of the fragment negative ions ([M – H]–, [M – 2H]–, [M – СО]–, [M – СОH]–, [M – СООH]– etc.) were predicted by means of analysis of decay channels for the molecular negative ions using the results of density functional theory calculations. Mean lifetime for molecular negative ions of 4.7-dihydroxycoumarin relative to electron autodetachment was measured. The adiabatic electron affinity (EAa) was estimated in the framework of the Arrhenius approximation. It was found that EAa values calculated at B3LYP/6-31+G(d) level with minimal addition of diffuse functions as a difference between the total energies of a neutral molecule and its radical anion correlate with experimental EAa values.

Dissociative electron attachment to benzoic acid (C7H6O2)

The dissociative electron attachment (DEA) to benzoic acid (C6H5COOH) has been studied using an experimental crossed beam setup of a quadrupole mass spectrometer and a trochoidal electron monochromator. Relative partial cross sections for the DEA to produce negative ion fragments show the main channels for dissociation. The comparison of the present results with the ultraviolet photoelectron spectrum of benzoic acid [J. Meeks, A. Wahlborg, and S. P. McGlynn, J. Electron Spectrosc. Relat. Phenom. 22, 43 (1981)] implies that most DEA bands in the high energy range are due to Feshbach resonances with double occupation of diffuse Rydberg-like orbitals. The measurements are supported by density functional theory calculations of the threshold energies.

NEGATIVE ION MASS SPECTROMETRY FOR THE ANALYSIS OF N-LINKED GLYCANS.

N-glycans from glycoproteins are complex, branched structures whose structural determination presents many analytical problems. Mass spectrometry, usually conducted in positive ion mode, often requires extensive sample manipulation, usually by derivatization such as permethylation, to provide the necessary structure-revealing fragment ions. The newer but, so far, lesser used negative ion techniques, on the contrary, provide a wealth of structural information not present in positive ion spectra that greatly simplify the analysis of these compounds and can usually be conducted without the need for derivatization. This review describes the use of negative ion mass spectrometry for the structural analysis of N-linked glycans and emphasises the many advantages that can be gained by this mode of operation. Biosynthesis and structures of the compounds are described followed by methods for release of the glycans from the protein. Methods for ionization are discussed with emphasis on matrix-assisted laser desorption/ionization (MALDI) and methods for producing negative ions from neutral compounds. Acidic glycans naturally give deprotonated species under most ionization conditions. Fragmentation of negative ions is discussed next with particular reference to those ions that are diagnostic for specific features such as the branching topology of the glycans and substitution positions of moieties such as fucose and sulfate, features that are often difficult to identify easily by conventional techniques such as positive ion fragmentation and exoglycosidase digestions. The advantages of negative over positive ions for this structural work are emphasised with an example of a series of glycans where all other methods failed to produce a structure. Fragmentation of derivatized glycans is discussed next, both with respect to derivatives at the reducing terminus of the molecules, and to methods for neutralization of the acidic groups on sialic acids to both stabilize them for MALDI analysis and to produce the diagnostic fragments seen with the neutral glycans. The use of ion mobility, combined with conventional mass spectrometry is described with emphasis on its use to extract clean glycan spectra both before and after fragmentation, to separate isomers and its use to extract additional information from separated fragment ions. A section on applications follows with examples of the identification of novel structures from lower organisms and tables listing the use of negative ions for structural identification of specific glycoproteins, glycans from viruses and uses in the biopharmaceutical industry and in medicine. The review concludes with a summary of the advantages and disadvantages of the technique. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

A unified statistical RRKM approach to the fragmentation and autoneutralization of metastable molecular negative ions of hexaazatrinaphthylenes.

For the compounds promising for use as n-type semiconductors in organic electronics and energy storage devices, hexaazatrinaphthylene (HATNA) and its derivative hexamethoxy-hexaazatrinaphthylene (HMHATA), the monomolecular processes occurring under the exposure of molecules to low-energy (0-15 eV) free electrons were studied by means of resonant electron capture negative ion mass spectrometry. Resonant electron attachment results in the formation of eminently long-lived molecular negative ions (MNIs) in an abnormally wide range of incident electron energy (Ee) from 0 to 5-7 eV. For both compounds, this observation serves as an indication of the strong electron-accepting properties and high stability of MNIs against electron autodetachment. A weak yield of the only fragment NIs, dehydrogenated anions, was detected for HATNA at Ee > 6 eV. MNIs of HMHATA are less stable to dissociative decay because of the presence of weakly bound terminal substituents. This is evidenced by the mass spectral observation of intense fragmentation occurring above Ee≈ 1 eV and leading to a loss of up to 3 methyl groups as the Ee increases. A series of metastable NI peaks observed in the mass spectra testify to the delayed and sequential nature of fragmentation. Based on the principles of statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory, the theoretical model of dissociative decay of NIs was developed and then adopted to quantify the rates of ground-state anion decay via electron autodetachment. The experimentally measured electron autodetachment lifetimes and fragmentation rates were best reproduced by the model at molecular adiabatic electron affinities preset to 2.15 eV for HATNA and 1.88 eV for HMHATA, in reasonable agreement with the quantum chemical DFT PBE/3ζ predictions.

Formation of positive and negative ions in the gas phase of D-ribose by low-energy electrons

SynopsisUsing a hypocycloidal electron spectrometer the total dissociative electron attachment cross section and the ionization cross section for D-ribose molecule were studied in the E<30 eV energy range. A clear structure near zero energy and in the 6.0-9.5 eV range is observed in the dissociative electron attachment cross section. These features appear due to the formation of negative ion fragments of the molecule. The ionization potential of the D-ribose molecule was determined at 9.74 ± 0.02 eV. In the total ionization cross section weak features are observed, which most likely due to the formation of positive ion fragments of the initial molecule.

Dissociation of furan-2-carboxylic acid by low energy electrons

SynopsisElectron attachment to molecular target can lead to a variety of negative fragment ions. We experimentally probe the main dissociative electron attachment channels in furan-2-carboxylic acid (C3H3O2 – COOH) - a molecular target composed of two important structural units: a furan ring and a carboxylic group. In our studies we utilise nearly mono-energetic electrons at electron energies from 0 eV up to 15 eV. Our detection setup is based on extraction lens system and quadrupole mass spectrometer, that enables measurement of the energy dependent mass-selected yields of newly formed stable anions.

Resonant electron capture by Captopril molecules

The modified dipeptide, Captopril, was studied to determine the effect of lateral functional groups on the decay of biomolecules in resonant reactions of electrons with molecules. The main channels of fragmentation of negative molecular ions were determined, and the characteristic fragment ions were identified. The SH fragment of the lateral substituent of cysteine plays an important role similarly as does the carboxyl fragment of aspartic acid in oligopeptides.

Linkage and sequence analysis of neutral oligosaccharides by negative-ion MALDI tandem mass spectrometry with laser-induced dissociation

Mass spectrometry (MS) has become the primary method for high-sensitivity structural determination of oligosaccharides. Fragmentation in the negative-ion MS can provide a wealth of structural information and these can be used for sequence determination. However, although negative-ion MS of neutral oligosaccharide using the deprotonated molecule [M−H]− as the precursor has been very successful for electrospray ionization (ESI), it has only limited success for matrix-assisted laser desorption/ionization (MALDI). In the present study, the features of negative-ion MALDI primary spectra were investigated in detail and the product-ion spectra using [M−H]– and [M+Cl]– as the precursors were carefully compared. The formation of [M−H]– was the main difficulty for MALDI while [M+Cl]– was proved to be useful as alternative precursor anion for MALDI-MS/MS to produce similar fragmentation for sequencing of neutral oligosaccharides. N-(1-naphthyl)ethylenediamine dihydrochloride was then used as both the matrix and the Cl− dopant to evaluate the extent of structural information that can be obtained by negative-ion fragmentation from [M+Cl]– using laser-induced dissociation (LID)-MS/MS for linkage assignment of gluco-oligosaccharides and for typing of blood-group ABO(H) and Lewis antigens on either type 1 or type 2 backbone-chains.

Secondary electron-induced biomolecular fragmentation in fast heavy-ion irradiation of microdroplets of glycine solution.

The influence of secondary electrons on radiation damage of biomolecules in water was studied by fast heavy-ion irradiation of biomolecular solutions. Water microdroplets containing the amino acid glycine under vacuum were irradiated by fast carbon projectiles with energies of 0.8-8.0 MeV. A variety of fragments from the droplets were observed by time-of-flight secondary-ion mass spectrometry: methylene amine cation and formate anion originating from the cleavage of C-Cα bonds, cyanide anion generated by cleavage of multiple bonds, and protonated and deprotonated glycine. The dependence of the yield of each fragment on projectile energy was examined; different behavior was observed for positive and negative fragments. Considering that biomolecular fragmentation may be induced by secondary electrons ejected from the water molecules surrounding biomolecules, we calculated the cross section for ejection of secondary electrons from liquid water. We found that the formation of both positive and negative glycine fragment ions correlated with the predicted emission of secondary electrons at different projectile energies. The formation of [Gly-H]- fragments, typical for gas phase dissociative electron attachment to amino acids, is shown to be caused by electrons from the low-energy part of the secondary electron distribution.

Resonant electron capture by uridine and deoxyuridine molecules: Fragmentation with charge transfer.

Charge transfer via DNA plays an important role in physical and chemical processes in biological systems, and is used in biomolecular electronics. The present study considers the resonant interaction of free electrons with nucleosides, which is important for an understanding of the processes of electron transport in DNA. Resonant electron capture negative ion mass spectrometry was used to study the processes of low-energy electron attachment to two uracil nucleosides, uridine and deoxyuridine, while density functional theory (DFT) calculations were used to analyze the energy aspects of ion formation and decay. Short-lived molecular ions, formed via mechanisms of π* shape resonances, were found in the energy region below 5 eV. The fragmentation channels of these resonances and the structures of the charged and neutral products formed were determined. These results suggest that the formation of some fragment negative ions occurs through intramolecular charge transfer.