Experimental and Trajectory Study on the Reaction of Protonated Methionine with Electronically Excited Singlet Molecular Oxygen (a1Δg): Reaction Dynamics and Collision Energy Effects

Effects of Intra-Base Pair Proton Transfer on Dissociation and Singlet Oxygenation of 9-Methyl-8-Oxoguanine-1-Methyl-Cytosine Base-Pair Radical Cations

8-Oxoguanosine is the most common oxidatively generated base damage and pairs with complementary cytidine within duplex DNA. The 8-oxoguanosine-cytidine lesion, if not recognized and removed, not only leads to G-to-T transversion mutations but renders the base pair being more vulnerable to the ionizing radiation and singlet oxygen (1 O2 ) damage. Herein, reaction dynamics of a prototype Watson-Crick base pair [9MOG ⋅ 1MC]⋅+ , consisting of 9-methyl-8-oxoguanine radical cation (9MOG⋅+ ) and 1-methylcystosine (1MC), was examined using mass spectrometry coupled with electrospray ionization. We first detected base-pair dissociation in collisions with the Xe gas, which provided insight into intra-base pair proton transfer of 9MOG⋅+  ⋅ 1MC← → ${{\stackrel{ {\rightarrow} } { {\leftarrow} } } }$ [9MOG - HN1 ]⋅ ⋅ [1MC+HN3' ]+ and subsequent non-statistical base-pair separation. We then measured the reaction of [9MOG ⋅ 1MC]⋅+ with 1 O2 , revealing the two most probable pathways, C5-O2 addition and HN7 -abstraction at 9MOG. Reactions were entangled with the two forms of 9MOG radicals and base-pair structures as well as multi-configurations between open-shell radicals and 1 O2 (that has a mixed singlet/triplet character). These were disentangled by utilizing approximately spin-projected density functional theory, coupled-cluster theory and multi-referential electronic structure modeling. The work delineated base-pair structural context effects and determined relative reactivity toward 1 O2 as [9MOG - H]⋅>9MOG⋅+ >[9MOG - HN1 ]⋅ ⋅ [1MC+HN3' ]+ ≥9MOG⋅+  ⋅ 1MC.

Singlet O2 Oxidation of the Radical Cation versus the Dehydrogenated Neutral Radical of 9-Methylguanine in a Watson-Crick Base Pair. Consequences of Structural Context

In DNA, guanine is the most susceptible to oxidative damage by exogenously and endogenously produced electronically excited singlet oxygen (¹O₂). The reaction mechanism and the product outcome strongly depend on the nucleobase ionization state and structural context. Previously, exposure of a monomeric 9-methylguanine radical cation (9MG^•+, a model guanosine compound) to ¹O₂ was found to result in the formation of an 8-peroxide as the initial product. The present work explores the ¹O₂ oxidation of 9MG^•+ and its dehydrogenated neutral form [9MG - H]^• within a Watson-Crick base pair consisting of one-electron-oxidized 9-methylguanine-1-methylcytosine [9MG·1MC]^•+. Emphasis is placed on entangling the base pair structural context and intra-base pair proton transfer with and consequences thereof on the singlet oxygenation of guanine radical species. Electrospray ionization coupled with guided-ion beam tandem mass spectrometry was used to study the formation and reaction of guanine radical species in the gas phase. The ¹O₂ oxidation of both 9MG^•+ and [9MG - H]^• is exothermic and proceeds barrierlessly either in an isolated monomer or within a base pair. Single- and multi-referential theories were tested for treating spin contaminations and multi-configurations occurring in radical-¹O₂ interactions, and reaction potential energy surfaces were mapped out to support experimental findings. The work provides a comprehensive profile for the singlet oxygenation of guanine radicals in different charge states and in the absence and the presence of base pairing. All results point to an 8-peroxide as the major oxidation product in the experiment, and the oxidation becomes slightly more favorable in a neutral radical form. On the basis of a variety of reaction pathways and product profiles observed in the present and previous studies, the interplay between guanine structure, base pairing, and singlet oxygenation and its biological implications are discussed.

Probing the Transition State-to-Intermediate Continuum: Mechanistic Distinction between a Dry versus Wet Perepoxide in the Singlet Oxygen "Ene" Reaction at the Air-Water Interface

A mechanistic study is reported for the reactions of singlet oxygen (¹O₂) with alkene surfactants of tunable properties. Singlet oxygen was generated either top-down (photochemically) by delivery as a gas to an air-water interface or bottom-up (chemically) by transport to the air-water interface as a solvated species. In both cases, reactions were carried out in the presence of 7-carbon (7C), 9-carbon (9C), or 11-carbon (11C) prenylsurfactants [(CH₃)₂C═CH(CH₂)_nSO₃^- Na⁺ (n = 4, 6, 8)]. Higher "ene" hydroperoxide regioselectivities (secondary ROOH 2 to tertiary ROOH 3) were reached in delivering ¹O₂ top-down through air as compared to bottom-up via aqueous solution. In the photochemical reaction, ratios of 2:3 increased from 2.5:1 for 7C, to 2.8:1 for 9C, and to 3.2:1 for 11C. In contrast, in the bubbling system that generated ¹O₂ chemically, the selectivity was all but lost, ranging only from 1.3:1 to 1:1. The phase-dependent regioselectivities appear to be correlated with the "ene" reaction with photochemically generated, drier ¹O₂ at the air-water interface vs those with wetter ¹O₂ from the bubbling reactor. Density functional theory-calculated reaction potential energy surfaces (PESs) were used to help rationalize the reaction phase dependence. The reactions in the gas phase are mediated by perepoxide transition states with 32-41 kJ/mol binding energy for C═C(π)···¹O₂. The perepoxide species, however, evolve to well-defined stationary structures in the aqueous phase, with covalent C-O bonds and 85-88 kJ/mol binding energy. The combined experimental and computational evidence points to a unique mechanism for ¹O₂ "ene" tunability in a perepoxide continuum from a transition state to an intermediate.

Singlet O2 Reactions with Radical Cations of 8-Bromoguanine and 8-Bromoguanosine: Guided-Ion Beam Mass Spectrometric Measurements and Theoretical Treatments

8-Bromoguanosine is generated in vivo as a biomarker for early inflammation. Its formation and secondary reactions lead to a variety of biological sequelae at inflammation sites, most of which are mutagenic and linked to cancer. Herein, we report the formation of radical cations of 8-bromoguanine (8BrG^•+) and 8-bromoguanosine (8BrGuo^•+) and their reactions toward the lowest excited singlet molecular oxygen (¹O₂)─a common reactive oxygen species generated in biological systems. This work aims to investigate synergistic, oxidatively generated damage of 8-brominated guanine and guanosine that may occur upon ionizing radiation, one-electron oxidation, and ¹O₂ oxidation. Capitalizing on measurements of reaction product ions and cross sections of 8BrG^•+ and 8BrGuo^•+ with ¹O₂ using guided-ion beam tandem mass spectrometry and augmented by computational modeling of the prototype reaction system, 8BrG^•+ + ¹O₂, using the approximately spin-projected ωB97XD/6-31+G(d,p) density functional theory, the coupled cluster DLPNO-CCSD(T)/aug-cc-pVTZ and the multireference CASPT2(21,15)/6-31G**, probable reaction products, and potential energy surfaces (PESs) were mapped out. 8BrG^•+ and 8BrGuo^•+ present similar exothermic oxidation products, and their reaction efficiencies with ¹O₂ increase with decreasing collision energy. Both single- and multireference theories predicted that the two most energetically favorable reaction pathways correspond to ¹O₂-addition to the C8 and C5-positions of 8BrG^•+, respectively. The CASPT2-calculated PES represents the best quantitative agreement with the experimental benchmark, in that the oxidation exothermicity is close to the water hydration energy of product ions and, thus, is able to eliminate a water ligand in the product ions.

Singlet Oxygen Oxidation of the Radical Cations of 8-Oxo-2'-deoxyguanosine and Its 9-Methyl Analogue: Dynamics, Potential Energy Surface, and Products Mediated by C5-O2 -Addition

8-Oxo-2'-deoxyguanosine (OG) is the most common DNA lesion. Notably, OG becomes more susceptible to oxidative damage than the undamaged nucleoside, forming mutagenic products in vivo. Herein the reactions of singlet O₂ with the radical cations of 8-oxo-2'-deoxyguanosine (OG^.+ ) and 9-methyl-8-oxoguanine (9MOG^.+ ) were investigated using ion-molecule scattering mass spectrometry, from which barrierless, exothermic O₂ -addition products were detected for both reaction systems. Corroborated by static reaction potential energy surface constructed using multi-reference CASPT2 theory and molecular dynamics simulated in the presence of the reactants' kinetic and internal energies, the C5-terminal O₂ -addition was pinpointed as the most probable reaction pathway. By elucidating the reaction mechanism, kinetics and dynamics, and reaction products and energetics, this work constitutes the first report unraveling the synergetic damage of OG by ionizing radiation and singlet O₂ .

Reaction Kinetics, Product Branching, and Potential Energy Surfaces of 1O2-Induced 9-Methylguanine-Lysine Cross-Linking: A Combined Mass Spectrometry, Spectroscopy, and Computational Study

We report a kinetics and mechanistic study on the ¹O₂ oxidation of 9-methylguanine (9MG) and the cross-linking of the oxidized intermediate 2-amino-9-methyl-9H-purine-6,8-dione (9MOG^OX) with N^α-acetyl-lysine-methyl ester (abbreviated as LysNH₂) in aqueous solutions of different pH. Experimental measurements include the determination of product branching ratios and reaction kinetics using mass spectrometry and absorption spectroscopy, and the characterization of product structures by employing collision-induced dissociation. Strong pH dependence was revealed for both 9MG oxidation and the addition of nucleophiles (water and LysNH₂) at the C5 position of 9MOG^OX. The ¹O₂ oxidation rate constant of 9MG was determined to be 3.6 × 10⁷ M^-1·s^-1 at pH 10.0 and 0.3 × 10⁷ M^-1·s^-1 at pH 7.0, both of which were measured in the presence of 15 mM LysNH₂. The ωB97XD density functional theory coupled with various basis sets and the SMD implicit solvation model was used to explore the reaction potential energy surfaces for the ¹O₂ oxidation of 9MG and the formation of C5-water and C5-LysNH₂ adducts of 9MOG^OX. Computational results have shed light on reaction pathways and product structures for the different ionization states of the reactants. The present work has confirmed that the initial ¹O₂ addition represents the rate-limiting step for the oxidative transformations of 9MG. All of the downstream steps are exothermic with respect to the starting reactants. The C5-cross-linking of 9MOG^OX with LysNH₂ significantly suppressed the formation of spiroiminodihydantoin (9MSp) resulting from the C5-water addition. The latter became dominant only at the low concentration (∼1 mM) of LysNH₂.

Singlet O2 Oxidation of a Deprotonated Guanine-Cytosine Base Pair and Its Entangling with Intra-Base-Pair Proton Transfer

We report an experimental and computational study on the ¹ O₂ oxidation of gas-phase deprotonated guanine-cytosine base pair [G ⋅ C-H]^- that is composed of 9HG ⋅ [C-H]^- and 7HG ⋅ [C-H]^- (pairing 9H- or 7H-guanine with N1-deprotonated cytosine), and 9HG ⋅ [C-H]^- _PT and 7HG ⋅ [C-H]^- _PT (formed by intra-base-pair proton transfer from the N1 of guanine to the N3 of [C-H]^- ). The conformer-averaged reaction product ions and cross section were measured over a center-of-mass collision energy range from 0.1 to 0.5 eV using a guided-ion-beam tandem mass spectrometer. To explore conformation-specific reactivity, collision dynamics of ¹ O₂ with each of the four [G ⋅ C-H]^- conformers was simulated at B3LYP/6-31G(d). Trajectories showed that the ¹ O₂ oxidation of the base pair entangles with intra-base-pair proton transfer, and prefers to occur in a collision when the base pair adopts a proton-transferred structure; trajectories also indicate that the 9HG-containing base pair favors stepwise formation of 4,8-endoperoxide of guanine, whereas the 7HG-containing base pair prefers concerted formation of guanine 5,8-endoperoxide. Using trajectory results as a guide, potential energy surfaces (PESs) along all possible reaction pathways were established using the approximately spin-projected ωB97XD/6-311++G(d,p)//B3LYP/6-311++G(d,p) method. PESs have not only rationalized trajectory findings but provided more accurate energetics and indicated that the proton-transferred base-pair conformers have lower activation barriers for oxidation than their non-proton-transferred counterparts.

Lysozyme oxidation by singlet molecular oxygen: Peptide characterization using [18 O]-labeling oxygen and nLC-MS/MS

Singlet molecular oxygen (¹ O₂ ) is generated in biological systems and reacts with different biomolecules. Proteins are a major target for ¹ O₂ , and His, Tyr, Met, Cys, and Trp are oxidized at physiological pH. In the present study, the modification of lysozyme protein by ¹ O₂ was investigated using mass spectrometry approaches. The experimental findings showed methionine, histidine, and tryptophan oxidation. The experiments were achieved using [¹⁸ O]-labeled ¹ O₂ released from thermolabile endoperoxides in association with nano-scale liquid chromatography coupled to electrospray ionization mass spectrometry. The structural characterization by nLC-MS/MS of the amino acids in the tryptic peptides of the proteins showed addition of [¹⁸ O]-labeling atoms in different amino acids.

Capturing Transient Endoperoxide in the Singlet Oxygen Oxidation of Guanine

The chemistry of singlet O2 toward the guanine base of DNA is highly relevant to DNA lesion, mutation, cell death, and pathological conditions. This oxidative damage is initiated by the formation of a transient endoperoxide through the Diels-Alder cycloaddition of singlet O2 to the guanine imidazole ring. However, no endoperoxide formation was directly detected in native guanine or guanosine, even at -100 °C. Herein, gas-phase ion-molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with singlet O2 at ambient temperature. Corroborated by results from potential energy surface exploration, kinetic modeling, and dynamics simulations, various aspects of endoperoxide formation and transformation (including its dependence on guanine ionization and hydration states, as well as on collision energy) were determined. This work has pieced together reaction mechanisms, kinetics, and dynamics data concerning the early stage of singlet O2 induced guanine oxidation, which is missing from conventional condensed-phase studies.

Mechanistic and Kinetic Study of Singlet O2 Oxidation of Methionine by On-Line Electrospray Ionization Mass Spectrometry

We report a reaction apparatus developed to monitor singlet oxygen ((1)O2) reactions in solution using on-line ESI mass spectrometry and spectroscopy measurements. (1)O2 was generated in the gas phase by the reaction of H2O2 with Cl2, detected by its emission at 1270 nm, and bubbled into aqueous solution continuously. (1)O2 concentrations in solution were linearly related to the emission intensities of airborne (1)O2, and their absolute scales were established based on a calibration using 9,10-anthracene dipropionate dianion as an (1)O2 trapping agent. Products from (1)O2 oxidation were monitored by UV-Vis absorption and positive/negative ESI mass spectra, and product structures were elucidated using collision-induced dissociation-tandem mass spectrometry. To suppress electrical discharge in negative ESI of aqueous solution, methanol was added to electrospray via in-spray solution mixing using theta-glass ESI emitters. Capitalizing on this apparatus, the reaction of (1)O2 with methionine was investigated. We have identified methionine oxidation intermediates and products at different pH, and measured reaction rate constants. (1)O2 oxidation of methionine is mediated by persulfoxide in both acidic and basic solutions. Persulfoxide continues to react with another methionine, yielding methionine sulfoxide as end-product albeit with a much lower reaction rate in basic solution. Density functional theory was used to explore reaction potential energy surfaces and establish kinetic models, with solvation effects simulated using the polarized continuum model. Combined with our previous study of gas-phase methionine ions with (1)O2, evolution of methionine oxidation pathways at different ionization states and in different media is described.

How protonation and deprotonation of 9-methylguanine alter its singlet O2 addition path: about the initial stage of guanine nucleoside oxidation

Protonated and deprotonated 9-methylguanine follow completely different oxidation routes.

Alternatives to the 'water oxidation pathway' of biological ozone formation

Recent studies have shown that ozone (O3) is endogenously generated in living tissues, where it makes both positive and negative physiological contributions. A pathway for the formation of both O3 and hydrogen peroxide (H2O2) was previously proposed, beginning with the antibody or amino acid-catalyzed oxidation of water by singlet oxygen ((1)O2) to form hydrogen trioxide (H2O3) as a key intermediate. A key pillar of this hypothesis is that some of the H2O2 molecules incorporate water-derived oxygen atoms. However, H2O3 decomposes extremely readily in water to form (1)O2 and water, rather than O3 and H2O2. This article highlights key literature indicating that the oxidation of organic molecules such as the amino acids methionine, tryptophan, histidine, and cysteine by (1)O2 is involved in ozone formation. Based on this, an alternative hypothesis for ozone formation is developed involving a further reaction of singlet oxygen with various oxidized organic intermediates. H2O2 having water-derived oxygen atoms is subsequently formed during ozone decomposition in water by known reactions.

Oxidation Dynamics of Methionine with Singlet Oxygen: Effects of Methionine Ionization and Microsolvation

We report an in-depth study on the gas-phase reactions of singlet O2[a(1)Δg] with methionine (Met) at different ionization and hydration states (including deprotonated [Met - H](-), hydrated deprotonated [Met - H](-)(H2O)1,2, and hydrated protonated MetH(+)(H2O)1,2), using guided-ion-beam scattering mass spectrometry. The measurements include the effects of collision energy (Ecol) on reaction cross sections over a center-of-mass Ecol range from 0.05 to 1.0 eV. The aim of this study is to probe the influences of Met ionization and hydration on its oxidation mechanism and dynamics. Density functional theory calculations, Rice-Ramsperger-Kassel-Marcus modeling, and quasi-classical, direct dynamics trajectory simulations were performed to examine the properties of various complexes and transition states that might be important along reaction coordinates, probe reaction potential energy surfaces, and to establish the atomic-level mechanism for the Met oxidation process. No oxidation products were observed for the reaction of [Met - H](-) with (1)O2 due to the high-energy barriers located in the product channels for this system. However, this nonreactive property was altered by the microsolvation of [Met - H](-); as a result, hydroperoxides were captured as the oxidation products for [Met - H](-)(H2O)1,2 + (1)O2. For the reaction of MetH(+)(H2O)1,2 + (1)O2, besides formation of hydroperoxides, an H2O2 elimination channel was observed. The latter channel is similar to what was found in the reaction of dehydrated MetH(+) with (1)O2 (J. Phys. Chem. B 2011, 115, 2671). The reactions of hydrated protonated and deprotonated Met are all inhibited by Ecol, becoming negligible at Ecol ≥ 0.5 eV. The kinetic and dynamical consequences of microsolvation on Met oxidation and their biological implications are discussed.

Evolution of oxidation dynamics of histidine: non-reactivity in the gas phase, peroxides in hydrated clusters, and pH dependence in solution

Oxidation of histidine by (1)O2 is an important process associated with oxidative damage to proteins during aging, diseases and photodynamic therapy of tumors and jaundice, and photochemical transformations of biological species in the troposphere. However, the oxidation mechanisms and products of histidine differ dramatically in these related environments which range from the gas phase through aerosols to aqueous solution. Herein we report a parallel gas- and solution-phase study on the (1)O2 oxidation of histidine, aimed at evaluating the evolution of histidine oxidation pathways in different media and at different ionization states. We first investigated the oxidation of protonated and deprotonated histidine ions and the same systems hydrated with explicit water molecules in the gas phase, using guided-ion-beam-scattering mass spectrometry. Reaction coordinates and potential energy surfaces for these systems were established on the basis of density functional theory calculations, Rice-Ramsperger-Kassel-Marcus modeling and direct dynamics simulations. Subsequently we tracked the oxidation process of histidine in aqueous solution under different pH conditions, using on-line UV-Vis spectroscopy and electrospray mass spectrometry monitoring systems. The results show that two different routes contribute to the oxidation of histidine depending on its ionization states. In each mechanism hydration is essential to suppressing the otherwise predominant dissociation of reaction intermediates back to reactants. The oxidation of deprotonated histidine in the gas phase involves the formation of 2,4-endoperoxide and 2-hydroperoxide of imidazole. These intermediates evolve to hydrated imidazolone in solution, and the latter either undergoes ring-closure to 6α-hydoxy-2-oxo-octahydro-pyrrolo[2,3-d]imidazole-5-carboxylate or cross-links with another histidine to form a dimeric product. In contrast, the oxidation of protonated histidine is mediated by 2,5-endoperoxide and 5-hydroperoxide, which convert to stable hydrated imidazolone end-product in solution. The contrasting mechanisms and reaction efficiencies of protonated vs. deprotonated histidine, which lead to pH dependence in the photooxidation of histidine, are interpreted in terms of the chemistry of imidazole with (1)O2. The biological implications of the results are also discussed.

Collision dynamics of protonated N-acetylmethionine with singlet molecular oxygen (a(1)Δg): the influence of the amide bond and ruling out the complex-mediated mechanism at low energies

It has been proposed (J. Phys. Chem. B 2011, 115, 2671) that the ammonium group is involved in the gas-phase reaction of protonated methionine (MetH(+)) with singlet oxygen (1)O2, yielding hydrogen peroxide and a dehydro compound of MetH(+) where the -NH3(+) transforms into cyclic -NH2-. For the work reported, the gas-phase reaction of protonated N-acetylmethionine (Ac-MetH(+)) with (1)O2 was examined, including the measurements of reaction products and cross sections over a center-of-mass collision energy (Ecol) range from 0.05 to 1.0 eV using a guided-ion-beam apparatus. The aim is to probe how the acetylation of the ammonium group affects the oxidation chemistry of the ensuing Ac-MetH(+). Properties of intermediates, transition states, and products along the reaction coordinate were explored using density functional theory calculations and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. Direct dynamics trajectory simulations were carried out at Ecol of 0.05 and 0.1 eV using the B3LYP/4-31G(d) level of theory. In contrast to the highly efficient reaction of MetH(+) + (1)O2, the reaction of Ac-MetH(+) + (1)O2 is extremely inefficient, despite there being exoergic pathways. Two product channels were observed, corresponding to transfer of two H atoms from Ac-MetH(+) to (1)O2 (H2T), and methyl elimination (ME) from a sulfone intermediate complex. Both channels are inhibited by collision energies, becoming negligible at Ecol > 0.2 eV. Analysis of RRKM and trajectory results suggests that a complex-mediated mechanism might be involved at very low Ecol, but direct, nonreactive collisions prevail over the entire Ecol range and physical quenching of (1)O2 occurs during the early stage of collisions.

Mass spectrometry study of multiply negatively charged, gas-phase NaAOT micelles: how does charge state affect micellar structure and encapsulation?

We report the formation and characterization of multiply negatively charged sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) aggregates in the gas phase, by electrospray ionization of methanol/water solution of NaAOT followed by detection using a guided-ion-beam tandem mass spectrometer. Singly and doubly charged aggregates dominate the mass spectra with the compositions of [Na(n-z)AOT(n)](z-) (n = 1-18 and z = 1-2). Solvation by water was detected only for small aggregates [Na(n-1)AOT(n)H(2)O](-) of n = 3-9. Incorporation of glycine and tryptophan into [Na(n-z)AOT(n)](z-) aggregates was achieved, aimed at identifying effects of guest molecule hydrophobicity on micellar solubilization. Only one glycine molecule could be incorporated into each [Na(n-z)AOT(n)](z-) of n ≥ 7, and at most two glycine molecules could be hosted in that of n ≥ 13. In contrast to glycine, up to four tryptophan molecules could be accommodated within single aggregates of n ≥ 6. However, deprotonation of tryptophan significantly decrease its affinity towards aggregates. Collision-induced dissociation (CID) was carried out for mass-selected aggregate ions, including measurements of product ion mass spectra for both empty and amino acid-containing aggregates. CID results provide a probe for aggregate structures, surfactant-solute interactions, and incorporation sites of amino acids. The present data was compared with mass spectrometry results of positively charged [Na(n+z)AOT(n)](z+) aggregates. Contrary to their positive analogues, which form reverse micelles, negatively charged aggregates may adopt a direct micelle-like structure with AOT polar heads exposed and amino acids being adsorbed near the micellar outer surface.