Tautomerization and Dissociation of Molecular Peptide Radical Cations

Radical‐mediated dissociations of peptide radical cations have intriguing unimolecular gas phase chemistry, with cleavages of almost every bond of the peptide backbone and amino acid side chains in a competitive and apparently “stochastic” manner. Challenges of unraveling mechanistic details are related to complex tautomerizations prior to dissociations. Recent conjunctions of experimental and theoretical investigations have revealed the existence of non‐interconvertible isobaric tautomers with a variety of radical‐site‐specific initial structures, generated from dissociative electron transfer of ternary metal‐ligand‐peptide complexes. Their reactivity is influenced by the tautomerization barriers, perturbing the nature, location, or number of radical and charge site(s), which also determine the energetics and dynamics of the subsequent radical‐mediated dissociatons. The competitive radical‐ and charge‐induced dissociations are extremely dependent on charge density. Charge sequesting can reduce the charge densities on the peptide backbone and hence enhance the flexibility of structural rearrangement. Analysing the structures of precursors, intermediates and products has led to the discovery of many novel radical migration prior to peptide backbone and/or side chain fragmentations. Upon these successes, scientists will be able to build peptide cationic analogues/tautomers having a variety of well‐defined radical sites.     

Radical Stability Directs Electron Capture and Transfer Dissociation of β‐Amino Acids in Peptides

We report on the characteristics of the radical‐ion‐driven dissociation of a diverse array of β‐amino acids incorporated into α‐peptides, as probed by tandem electron‐capture and electron‐transfer dissociation (ECD/ETD) mass spectrometry. The reported results demonstrate a stronger ECD/ETD dependence on the nature of the amino acid side chain for β‐amino acids than for their α‐form counterparts. In particular, only aromatic (e.g., β‐Phe), and to a substantially lower extent, carbonyl‐containing (e.g., β‐Glu and β‐Gln) amino acid side chains, lead to N? C_β bond cleavage in the corresponding β‐amino acids. We conclude that radical stabilization must be provided by the side chain to enable the radical‐driven fragmentation from the nearby backbone carbonyl carbon to proceed. In contrast with the cleavage of backbones derived from α‐amino acids, ECD of peptides composed mainly of β‐amino acids reveals a shift in cleavage priority from the N? C_β to the C_α? C bond. The incorporation of CH₂ groups into the peptide backbone may thus drastically influence the backbone charge solvation preference. The characteristics of radical‐driven β‐amino acid dissociation described herein are of particular importance to methods development, applications in peptide sequencing, and peptide and protein modification (e.g., deamidation and isomerization) analysis in life science research.     

Arginine‐Facilitated α‐ and π‐Radical Migrations in Glycylarginyltryptophan Radical Cations

We have used model tripeptides GXW (with X being one of the amino acid residues glycine (G), alanine (A), leucine (L), phenylalanine (F), glutamic acid (E), histidine (H), lysine (K), or arginine (R)) to study the effects of the basicity of the amino acid residue on the radical migrations and dissociations of odd‐electron molecular peptide radical cations M^.+ in the gas phase. Low‐energy collision‐induced dissociation (CID) experiments revealed that the interconvertibility of the isomers [G^.XW]⁺ (radical centered on the N‐terminal α‐carbon atom) and [GXW]^.+ (radical centered on the π system of the indolyl ring) generally increased upon increasing the proton affinity of residue X. When X was arginine, the most basic amino acid, the two isomers were fully interconvertible and produced almost identical CID spectra despite the different locations of their initial radical sites. The presence of the very basic arginine residue allowed radical migrations to proceed readily among the [G^.RW]⁺ and [GRW]^.+ isomers prior to their dissociations. Density functional theory calculations revealed that the energy barriers for isomerizations among the α‐carbon‐centered radical [G^.RW]⁺, the π‐centered radical [GRW]^.+, and the β‐carbon‐centered radical [GRW_β^.]⁺ (ca. 32–36 kcal mol⁻¹) were comparable with those for their dissociations (ca. 32–34 kcal mol⁻¹). The arginine residue in these GRW radical cations tightly sequesters the proton, thereby resulting in minimal changes in the chemical environment during the radical migrations, in contrast to the situation for the analogous GGW system, in which the proton is inefficiently stabilized during the course of radical migration.     

Prompt and Slow Electron‐Detachment‐Dissociation/Electron‐Photodetachment‐Dissociation of a 21‐Mer Peptide

Electron detachment dissociation (EDD) and electron photodetachment dissociation (EPD) are relatively new dissociation methods that involve electron detachment followed by radical‐driven dissociation from multiply deprotonated species. EDD yields prompt dissociation whereas only electron detachment is obtained by EPD; subsequent vibrational activation of the charge‐reduced radical anion is required to obtain the product ions. Herein, the fragmentation patterns that were obtained by EDD and by vibrational activation of the charge‐reduced radical anions that were produced through EDD or EPD (activated‐EDD and activated‐EPD) were compared. The observed differences were related to the dissociation kinetics and/or the contribution of electron‐induced dissociation (EID). Time‐resolved double‐resonance experiments were performed to measure the dissociation rate constants of the EDD product ions. Differences in the formation kinetics were revealed between the classical EDD/EPD ′a^._i/′′x_j complementary ions and some ′a^._i/c_i/′′′z^._j product ions, which were produced with slower dissociation rate constants, owing to the presence of specific neighbouring side chains. A new fragmentation pathway is proposed for the formation of the slow‐kinetics ′a^._i ions.     

Boron Radical Cations from the Facile Oxidation of Electron‐Rich Diborenes

The realization of a phosphine‐stabilized diborene, Et₃P?(Mes)B?B(Mes)?PEt₃ ( 4 ), by KC₈ reduction of Et₃P?B₂Mes₂Br₂ in benzene enabled the evaluation and comparison of its electronic structure to the previously described NHC‐stabilized diborene IMe?(Dur)B?B(Dur)?IMe ( 1 ). Importantly, both species feature unusual electron‐rich boron centers. However, cyclic voltammetry, UV/Vis spectroscopy, and DFT calculations revealed a significant influence of the Lewis base on the reduction potential and absorption behavior of the B? B double bond system. Thus, the stronger σ‐donor strength and larger electronegativity of the NHC ligand results in an energetically higher‐lying HOMO, making 1 a stronger neutral reductant as 4 ( 1 : E_1/2=?1.55 V; 4 : ?1.05 V), and a smaller HOMO–LUMO gap of 1 accompanied by a noticeable red‐shift of its lowest‐energy absorption band with respect to 4 . Owing to the highly negative reduction potentials, 1 and 4 were easily oxidized to afford rare boron‐centered radical cations ( 5 and 6 ).     

Gas‐Phase Unimolecular Dissociation Reveals Dominant Base Property of Protonated Homocysteine Sulfinyl Radical Ions

Homocysteine sulfinyl radical (^SO?Hcy) is a reactive intermediate involved during oxidative damage of DNA in the presence of high concentrations of homocysteine (Hcy). The short lifetime of ^SO?Hcy makes its preparation, isolation, and characterization challenging using traditional chemical measurement tools. Herein, we demonstrate the first study on mass‐selected protonated ^SO?Hcy ions in the gas phase by investigating its unimolecular dissociation pathways from low energy collision‐induced dissociation (CID). Tandem mass spectrometry (MS/MS), stable‐isotope labeling, and theoretical calculations were employed to rationalize the observed fragmentation pathways. The dominant dissociation channel of protonated ^SO?Hcy was a charge‐directed H₂O loss from the protonated sulfinyl radical (‐SO?) moiety, forming a thiyl radical (‐S?), which further triggered sequential radical‐directed ?SH loss through multiple pathways. Compared to cysteine sulfinyl radical (^SO?Cys), the small structural change induced by one additional methylene group in the side chain of ^SO?Hcy significantly promotes its base property while reducing the radical reactivity of sulfinyl radical. This observation provides new insight into studying reactions of ^SO?Hcy with biomolecules, which are critical in understanding toxicity induced by high levels of Hcy in biological conditions.     

Resonance Energy Transfer Relates the Gas‐Phase Structure and Pharmacological Activity of Opioid Peptides

Enkephalins are efficient pain‐relief drugs that bind to transmembrane opioid receptors. One key structural parameter that governs the pharmacological activity of these opioid peptides and is typically determined from condensed‐phase structures is the distance between the aromatic rings of their Tyr and Phe residues. We use resonance energy transfer, detected by a combination of cold ion spectroscopy and mass spectrometry, to estimate the Tyr–Phe spacing for enkephalins in the gas phase. In contrast to the condensed‐phase structures, these distances appear to differ substantially in enkephalins with different pharmacological efficiencies, suggesting that gas‐phase structures might be a better pharmacophoric metric for ligand peptides.     

Single‐Electron Self‐Exchange between Cage Hydrocarbons and Their Radical Cations in the Gas Phase

We show that the radical cations of adamantane (C₁₀H₁₆^.+, 1 H^.+) and perdeuteroadamantane (C₁₀D₁₆^.+, 1 D^.+) are stable species in the gas phase. The radical cation of adamantylideneadamantane (C₂₀H₂₈^.+, 2 H^.+) is also stable (as in solution). By using the natural ¹³C abundances of the ions, we determine the rate constants for the reversible isergonic single‐electron transfer (SET) processes involving the dyads 1 H^.+/ 1 H, 1 D^.+/ 1 D and 2 H^.+/ 2 H. Rate constants for the reaction 1 H^.++ 1 D? 1 H+ 1 D^.+ are also determined and Marcus’ cross‐term equation is shown to hold in this case. The rate constants for the isergonic processes are extremely high, practically collision‐controlled. Ab initio computations of the electronic coupling (H_DA) and the reorganization energy (λ) allow rationalization of the mechanism of the process and give insights into the possible role of intermediate complexes in the reaction mechanism.     

Reproducibility Evaluation of Urinary Peptide Detection Using CE-MS

In recent years, capillary electrophoresis coupled to mass spectrometry (CE-MS) has been increasingly applied in clinical research especially in the context of chronic and age-associated diseases, such as chronic kidney disease, heart failure and cancer. Biomarkers identified using this technique are already used for diagnosis, prognosis and monitoring of these complex diseases, as well as patient stratification in clinical trials. CE-MS allows for a comprehensive assessment of small molecular weight proteins and peptides (<20 kDa) through the combination of the high resolution and reproducibility of CE and the distinct sensitivity of MS, in a high-throughput system. In this study we assessed CE-MS analytical performance with regards to its inter- and intra-day reproducibility, variability and efficiency in peptide detection, along with a characterization of the urinary peptidome content. To this end, CE-MS performance was evaluated based on 72 measurements of a standard urine sample (60 for inter- and 12 for intra-day assessment) analyzed during the second quarter of 2021. Analysis was performed per run, per peptide, as well as at the level of biomarker panels. The obtained datasets showed high correlation between the different runs, low variation of the ten highest average individual log2 signal intensities (coefficient of variation, CV < 10%) and very low variation of biomarker panels applied (CV close to 1%). The findings of the study support the analytical performance of CE-MS, underlining its value for clinical application.     

Photocatalytic Redox Reactions for In‐Source Peptide Fragmentation

In‐source oxidation : In‐source photocatalytic redox reactions for inducing peptide fragmentation are achieved on a TiO₂‐derived target plate during laser desorption ionization mass spectrometry in the presence of samples and glucose acting as both an electron donor and a hole conductor (see scheme).

     

Methane Activation Mediated by a Series of Cerium–Vanadium Bimetallic Oxide Cluster Cations: Tuning Reactivity by Doping

The reactions of cerium–vanadium cluster cations Ce_xV_yO_z⁺ with CH₄ are investigated by time‐of‐flight mass spectrometry and density functional theory calculations. (CeO₂)_m(V₂O₅)_n⁺ clusters (m=1,2, n=1–5; m=3, n=1–4) with dimensions up to nanosize can abstract one hydrogen atom from CH₄. The theoretical study indicates that there are two types of active species in (CeO₂)_m(V₂O₅)_n⁺, V[(O_t)₂]^. and [(O_b)₂CeO_t]^. (O_t and O_b represent terminal and bridging oxygen atoms, respectively); the former is less reactive than the latter. The experimentally observed size‐dependent reactivities can be rationalized by considering the different active species and mechanisms. Interestingly, the reactivity of the (CeO₂)_m(V₂O₅)_n⁺ clusters falls between those of (CeO₂)_2–4⁺ and (V₂O₅)_1–5⁺ in terms of C?H bond activation, thus the nature of the active species and the cluster reactivity can be effectively tuned by doping.     

The Remarkable Effect of the Manganese Ion with Dioxygen on the Stability of π‐Conjugated Radical Cations

In this paper, nanosecond laser flash photolysis has been used to investigate the influence of metal ions on the kinetics of radical cations of a range of carotenoids (astaxanthin (ASTA), canthaxanthin (CAN), and β‐carotene (β‐CAR)) and various electron donors (1,4‐diphenyl‐1,3‐butadiene (14DPB), 1,6‐diphenyl‐1,3,5‐hexatriene (16DPH), 4‐methoxy‐trans‐stilbene (4 MeOSt), and trans‐stilbene (trans‐St)) in benzonitrile. Radical cations have been generated by means of photosensitized electron‐transfer (ET) using 1,4‐dicyanonaphthalene (14DCN) and biphenyl (BP). The kinetic decay of CAR ^{. +} shows a strong dependence on the identity of the examined metal ion. For example, whereas NaClO₄ has a weak effect on the kinetics of CAR ^{. +}, Ni(ClO₄)₂ causes a strong retardation of the decay of CAR ^{. +}. It is also interesting to note that Mn²⁺, which is a biologically relevant metal ion, shows the strongest effect of all the investigated metal ions (e.g., in the presence of Mn²⁺ ions, the half‐life (t_1/2) of CAN ^{. +} (t_1/2>90 ms) is more than three orders of magnitude higher than in the absence of the metal ions (t_1/2≈16 μs)). Furthermore, the influence of metal‐ion and oxygen concentrations on the kinetics of CAR ^{. +} reveals their pronounced effect on the kinetic decay of CAR ^{. +}. However, these remarkable effects are greatly diminished if either oxygen or metal ions are removed from the investigated solutions. Therefore, it can be concluded that oxygen and metal ions interact cooperatively to induce the observed substantial effects on the stabilities of CAR ^{. +}. These results are the first direct observation of the major role of oxygen in the stabilization of radical cations, and they support the earlier mechanism proposed by Astruc et al. for the role of oxygen in the inhibition of cage reactions. On the basis of these results, the factors that affect the stability of radical cations are discussed and the mechanism that shows the role of oxygen and metal ions in the enhancement of radical‐cation stability is described.     

Living Radical Polymerization as a Tool for the Synthesis of Polymer‐Protein/Peptide Bioconjugates

Combinations of synthetic and natural macromolecules offer a route to new functional materials. While biological and polymer chemistry may not be natural bedfellows, many researchers are focusing their attention on the benefits of combining these fields. Recent advances in living radical polymerization have provided methods to build tailor‐made macromolecular moieties using relatively simple processes. This has led to a plethora of block copolymers, end‐functional polymers and polymers with a whole range of biological recognition abilities. This review covers work carried out until late 2006 combining living radical polymerization with proteins and peptides in the rapidly‐expanding field of bioconjugation.

     

Synthesis and Characterization of Acetylene‐Linked Bisphenalenyl and Metallic‐Like Behavior in Its Charge‐Transfer Complex

We prepared and isolated a phenalenyl‐based neutral hydrocarbon ( 1 b ) with a biradical index of 14 %, as well as its charge‐transfer (CT) complex 1 b –F₄‐TCNQ. The crystal structure and the small HOMO–LUMO gap assessed by electrochemical and optical methods support the singlet‐biradical contribution to the ground state of the neutral 1 b . This biradical character suggests that 1 b has the electronic structure of phenalenyl radicals coupled weakly through an acetylene linker, that is, some independence of the two phenalenyl moieties. The monocationic species 1 b^{. +} was obtained by reaction with the organic electron acceptor F₄‐TCNQ. The cationic species has a small disproportionation energy ΔE for the reaction 2× 1 b^{. +}? 1 b + 1 b ²⁺, which presumably originates from the independence of the phenalenyl moieties. The small ΔE led to a small on‐site Coulombic repulsion U_eff=0.61 eV in the CT complex. Moreover, a very effective orbital overlap of the phenalenyl rings between molecules afforded a relatively large transfer integral t=0.09 eV. The small U_eff/4t ratio (=1.7) resulted in a metallic‐like conductive behavior at around room temperature. Below 280 K, the CT complex showed a transition into a semiconductive state as a result of bond formation between phenalenyl and F₄‐TCNQ carbon atoms.