UV‐vis spectroscopy of gas‐phase ions Tureček, František
Mass spectrometry reviews,
January/February 2023, 2023-01-00, 20230101, Letnik:
42, Številka:
1
Journal Article
Recenzirano
Photodissociation action spectroscopy has made a great progress in expanding investigations of gas‐phase ion structures. This review deals with aspects of gas‐phase ion electronic excitations that ...result in wavelength‐dependent dissociation and light emission via fluorescence, chiefly covering the ultraviolet and visible regions of the spectrum. The principles are briefly outlined and a few examples of instrumentation are presented. The main thrust of the review is to collect and selectively present applications of UV‐vis action spectroscopy to studies of stable gas‐phase ion structures and combinations of spectroscopy with ion mobility, collision‐induced dissociation, and ion–ion reactions leading to the generation of reactive intermediates and electronic energy transfer.
Gas-phase chemistry of cation radicals related to ionized nucleic acids has enjoyed significant recent progress thanks to the development of new methods for cation radical generation, ion ...spectroscopy, and reactivity studies. Oxidative methods based on intramolecular electron transfer in transition-metal complexes have been used to generate nucleobase and nucleoside cation radicals. Reductive methods relying on intermolecular electron transfer in gas-phase ion–ion reactions have been utilized to generate a number of di- and tetranucleotide cation radicals, as well as charge-tagged nucleoside radicals. The generated cation radicals have been studied by infrared and UV–visible action spectroscopy and ab initio and density functional theory calculations, providing optimized structures, harmonic frequencies, and excited-state analysis. This has led to the discovery of stable noncanonical nucleobase cation radicals of unusual electronic properties and extremely low ion–electron recombination energies. Intramolecular proton-transfer reactions in cation radical oligonucleotides and Watson–Crick nucleoside pairs have been studied experimentally, and their mechanisms have been elucidated by theory. Whereas the range of applications of the oxidative methods is currently limited to nucleobases and readily oxidizable guanosine, the reductive methods can be scaled up to generate large oligonucleotide cation radicals including double-strand DNA. Challenges in the experimental and computational approach to DNA cation radicals are discussed.
How I have learnt to ignore bibliometrics Tureček, František
Mass spectrometry reviews,
May/June 2024, 2024 May-Jun, 2024-05-00, 20240501, Letnik:
43, Številka:
3
Journal Article
Photochemical crosslinking in gas-phase ion complexes has been introduced as a method to study biomolecular structures and dynamics. Emphasis has been on carbene-based crosslinking induced by ...photodissociation of diazirine-tagged ions. The features that characterize gas-phase crosslinking include (1) complex formation in electrospray droplets that allows for library-type screening; (2) well defined stoichiometry of the complexes due to mass-selective isolation; (3) facile reaction monitoring and yield determination, and (4) post-crosslinking structure analysis by tandem mass spectrometry that has been combined with hydrogen-deuterium exchange, UV-vis action spectroscopy, and ion mobility measurements. In this account, examples are given of peptide-peptide, peptide-nucleotide, and peptide-ligand crosslinking that chiefly used carbene-based reactions. The pros and cons of gas-phase crosslinking are discussed. Nitrile-imine based crosslinking in gas-phase ions is introduced as a promising new approach to ion structure analysis that offers high efficiency and has the potential for wide ranging applications.
Crosslinking in gas-phase ions, augmented by tandem mass spectrometry and Born-Oppenheimer molecular dynamics calculations, provides analysis of structure and intermolecular interactions in peptide-peptide, peptide-nucleotide, and peptide-ligand complexes.
Cation radicals of guanine (G •+ ), 9-methylguanine (MG •+ ), and guanosine (rG •+ ) were generated by dissociative oxidation of gas-phase copper complexes and characterized by UV–vis ...photodissociation action spectra and ab initio calculations. Comparison of the action spectra of G •+ with the calculated vibronic absorption spectra of several cation radical tautomers showed the best match for the canonical 6-oxo-N-9-H structure (G1 •+ ). The formation of G1 •+ was favored by the stability of its precursor CuII ion complexes in solution and the gas phase. G1 •+ was the marginally lowest-energy guanine tautomer according to CCSD(T) calculations extrapolated to the complete basis set limit (CBS). A canonical 6-oxo structure (MG1 •+ ) was also assigned to the 9-methylguanine cation radical on the basis of a match between the action spectrum and the calculated vibronic absorption spectra. MG1 •+ was calculated by CCSD(T)/CBS to be marginally less stable than the 6-OH enol tautormer, but its formation was favored by the superior stability of its precursor CuII ion complexes in solution and the gas phase. Action spectroscopy allowed us to assign the canonical 6-oxo structure (rG1 •+ ) to the gas-phase guanosine cation radicals that were formed as the lowest-energy tautomers. The absorption bands in the action spectra were assigned on the basis of time-dependent density functional theory calculations that were benchmarked on equation-of-motion coupled cluster calculations of G •+ .
Excited electronic states in several radical chromophores representing photochemically active groups in peptide and protein radicals and cation radicals were investigated computationally using ...equation-of-motion coupled cluster (EOM-CCSD) and time-dependent density functional theory (TD-DFT) methods. The calculations identified the main transitions responsible for photodissociations of gas-phase peptide cation radicals in the near-UV region of the spectrum. Analysis of the EOM-CCSD benchmarks showed that no TD-DFT method was universally accurate across the various radical motifs that included Cα-amide, aminoketyl, formamidyl, guanidyl, carbamyl, benzyl, phenoxy, and tautomeric dihydrophenyl and imidazolyl radicals. Overall, the ωB97XD, M06-2X, and LC-BLYP hybrid functionals showed acceptable performance when benchmarked against EOM-CCSD calculations. However, the performance of these TD-DFT methods depended on the nature of the radical chromophore, emphasizing the need for benchmarking and careful analysis.
Oxidation of nontraditional nucleobases 1-methylcytosine (hachimoji base S) and isoguanine (hachimoji base B) in gas-phase ternary complexes with CuII(terpyridine)2+ formed cation radicals that were ...characterized by tandem mass spectrometry, UV–vis photodissociation action spectroscopy in the 210–700 nm region, and ab initio calculations up to the CCSD(T)/complete basis set level of theory. Oxidation of S was accompanied by exothermic isomerization in the 1-methylcytosine ion (1 +• ), forming 1-methylene-2-hydroxy-4-aminopyrimidine cation radical (9 +• ) as a noncanonical distonic isomer of the nucleobase. Ion 9 +• was characterized by deuterium exchange experiments and provided a matching UV–vis action spectrum with the vibronic absorption spectrum from time-dependent density functional theory calculations. Oxidation of B resulted in the formation of a canonical isoguanine cation radical (12 +• ) as judged from the match of the experimental action spectrum with the calculated vibronic absorption spectrum. The calculated adiabatic ionization energies of canonical S and B, 8.51 and 7.76 eV, respectively, indicated exothermic electron transfer from B to S +• to proceed in an ionized base pair. Contrasting this, the lowest energy tautomer of ionized S (9 +• ) had a low adiabatic recombination energy, REadiab = 5.70 eV, that would prevent it from oxidizing other nucleobases. Recombination energies of several nucleobase tautomers are reported and discussed.
We report a combined experimental and computational study of adenosine cation radicals that were protonated at adenine and furnished with a radical handle in the form of an acetoxyl radical, •CH2COO, ...that was attached to ribose 5′-O. Radicals were generated by collision-induced dissociation (CID) and characterized by tandem mass spectrometry and UV–vis photodissociation action spectroscopy. The acetoxyl radical was used to probe the kinetics of intramolecular hydrogen transfer from the ribose ring positions that were specifically labeled with deuterium at C1′, C2′, C3′, C4′, C5′, and in the exchangeable hydroxyl groups. Hydrogen transfer was found to chiefly involve 3′-H with minor contributions by 5′-H and 2′-H, while 4′-H was nonreactive. The hydrogen transfer rates were affected by deuterium isotope effects. Hydrogen transfer triggered ribose ring cleavage by consecutive dissociations of the C4′–O and C1′–C2′ bonds, resulting in expulsion of a C6H9O4 radical and forming a 9-formyladenine ion. Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations of unimolecular constants were carried out using the effective CCSD(T)/6-311++G(3d,2p) and M06-2X/aug-cc-pVTZ potential energy surfaces for major isomerizations and dissociations. The kinetic analysis showed that hydrogen transfer to the acetoxyl radical was the rate-determining step, whereas the following ring-opening reactions in ribose radicals were fast. Using DFT-computed energies, a comparison was made between the thermochemistry of radical reactions in adenosine and 2′-deoxyadenosine cation radicals. The 2′-deoxyribose ring showed lower TS energies for both the rate-determining 3′-H transfer and ring cleavage reactions.
Analysis of new psychoactive substances (NPS), which is essential for toxicological and forensic reasons, can be made complicated by the presence of isomers. Ion mobility has been used as a ...standalone technique or coupled to mass spectrometry to detect and identify NPS. However, isomer separation has so far chiefly relied on chromatography. Here we report on the determination of isomeric ratios using cyclic ion mobility-mass spectrometry without any chromatographic separation. Isomers were distinguished by mobility separation of lithium adducts. Alternatively, we used arrival time distribution (ATD) profiles that were characteristic of individual isomers and were acquired for protonated molecules or fragment ions. Both approaches provided comparable results. Calculations were used to determine the structures and collision cross sections of both protonated and lithiated isomers that accurately characterized their ion mobility properties. The applicability of ATD profiles to isomer differentiation was demonstrated using direct infusion and flow injection analysis with electrospray of solutions, as well as desorption electrospray of solid samples. Data processing was performed by applying multiple linear regression to the ATD profiles. Using the proposed ATD profile-based approach, the relationships between the determined and given content of isomers showed good linearity with coefficients of determination typically greater than 0.99. Flow injection analysis using an autosampler allowed us to rapidly determine isomeric ratios in a sample containing two isomeric pairs with a minor isomer of 10% (determined 9.3% of 3-MMC and 11.0% of 3-FMC in a mixture with buphedrone and 4-FMC). The proposed approach is not only useful for NPS, but also may be applicable to small isomeric molecules analyzed by ion mobility when complete separation of isomers is not achieved.
